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annotate mqppep_anova_script.Rmd @ 26:5b8e15b2a67c draft

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author eschen42
date Wed, 26 Oct 2022 23:48:51 +0000
parents f9cd87ac8006
children 42b207aaa527
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1 ---
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2 title: "MaxQuant Phosphoproteomic Enrichment Pipeline ANOVA/KSEA"
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3 author:
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4 - "Nick Graham^[ORCiD 0000-0002-6811-1941, University of Southern California: Los Angeles, CA, US]"
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5 - "Larry Cheng^[ORCiD 0000-0002-6922-6433, Rutgers School of Graduate Studies: New Brunswick, NJ, US]"
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6 - "Art Eschenlauer^[ORCiD 0000-0002-2882-0508, University of Minnesota: Minneapolis, Minnesota, US]"
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7 date:
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8 - "May 28, 2018"
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9 - "; revised June 23, 2022"
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10 lot: true
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11 output:
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12 pdf_document:
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13 toc: true
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14 toc_depth: 2
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15 keep_tex: true
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16 dev: pdf
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17 includes:
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18 in_header: mqppep_anova_preamble.tex
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19 latex_macros: false
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20 raw_tex: true
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21 urlcolor: blue
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22 params:
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23 alphaFile: "test-data/alpha_levels.tabular"
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24 inputFile: "test-data/test_input_for_anova.tabular"
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25 preprocDb: "test-data/test_input_for_anova.sqlite"
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26 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
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27 regexSampleNames: "\\.\\d+[A-Z]$"
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28 regexSampleGrouping: "\\d+"
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29 groupFilterPatterns: ".+"
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30 groupFilter: !r c("none", "exclude", "include")[1]
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31 imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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32 kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5]
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33 #imputationMethod: !r c("group-median", "median", "mean", "random")[1]
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34
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35 # how should sample groups be interpreted?
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36 # - "f": fixed patterns (like `grep -F`)
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37 # - "p": PERL-compatible (like `grep -P`)
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38 # - "r": extended grep patterns (like `grep -E`)
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39 # use what case sensitivity?
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40 # - "i": case insensitive matching (like `grep -i`)
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41 groupFilterMode: !r c("r", "ri", "p", "pi", "f", "fi")[1]
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42 # what pattern should be used for the first column
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43 # (extended grep pattern, case sensitive)
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44 firstDataColumn: "^Intensity[^_]"
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45 # for small random value imputation, what percentile should be center?
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46 meanPercentile: 50
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47 #meanPercentile: 1
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48 # for small random value imputation, what should `s / mean(x)` ratio be?
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49 sdPercentile: 1.0
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50 # output path for imputed data file
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51 imputedDataFilename: "test-data/limbo/imputedDataFilename.txt"
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52 # output path for imputed/quantile-normalized/log-transformed data file
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53 imputedQNLTDataFile: "test-data/limbo/imputedQNLTDataFile.txt"
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54 # output path for contents of `stats_metadata_v` table
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55 anovaKseaMetadata: "test-data/limbo/anovaKseaMetadata.txt"
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56 # how to test one variable with > 2 categories (e.g., aov or kruskal.test)
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57 oneWayManyCategories: !r c("aov", "kruskal.test", "oneway.test")[1]
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58 # how to test one variable with 2 categories (e.g., oneway.test)
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59 oneWayTwoCategories: !r c("aov", "kruskal.test", "oneway.test")[3]
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60 # what should be the minimum quality for consideration in both
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61 minQuality: 0
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62 # correct KSEA with FDR (recommended) or raw p-value
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63 kseaCutoffStatistic: !r c("FDR", "p.value")[1]
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64 # correct KSEA threshold 0.05 (conventional) or higher (perhaps better)
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65 # "perhaps better" meaning that KSEA is an hypothesis-generator, not -test
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66 #kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5)[1]
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67 # minimum number of substrates required for a kinase to be considered in KSEA
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68 kseaMinSubstrateCount: 1
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69 # Should KSEA be performed aggregating signed log2FC or absolute?
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70 # FALSE use raw log2FC for KSEA as for KSEAapp::KSEA.Scores
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71 # TRUE use abs(log2FC) for KSEA as Justin Drake requested; this is a
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72 # justifiable deviation from the KSEAapp::KSEA.Scores algorithm.
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73 kseaUseAbsoluteLog2FC: TRUE
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74 #kseaUseAbsoluteLog2FC: FALSE
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75 # minimum number of observed values per sample-group
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76 intensityMinValuesPerGroup: 1
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77 # maximum number of heatmap rows (result are poor when > 50)
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78 intensityHeatmapRows: 50
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79 # what should be the primary criterion to eliminate excessive heatmap rows
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80 intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1]
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81 # should correlation among substrates be used (rather than covariance)
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82 correlateSubstrates: TRUE
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83 # only show covariance among variables having variance > 1
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84 filterCovVarGT1: TRUE
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85 # maximum number of residues to display for ppeps in rownames or columnames
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86 ppepTruncN: 10
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87 # maximum number of characters of subgenes to display in rownames or columnames
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88 subgeneTruncN: 10
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89 # maximum number of characters for paste(subgene, ppep) for enrichment plots
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90 substTruncN: 20
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91 # should boxplots use variable-width boxes to reflect # of samples
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92 boxPlotVarWidth: TRUE
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93 # should boxplots use notched boxes to reflect difference between samples
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94 boxPlotNotch: TRUE
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95 # look-up tables for kinase descriptions
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96 kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2"
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97 kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2"
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98 # should debugging trace messages be printed?
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99 showEnrichedSubstrates: FALSE
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100
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101 # should debugging nb/nbe messages be printed?
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102 printNBMsgs: FALSE
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103 # should debugging trace messages be printed?
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104 printTraceMsgs: FALSE
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105 # when debugging files are needed, set debugFileBasePath to the path
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106 # to the directory where they should be writtn
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107 debugFileBasePath: !r if (TRUE) NULL else "test-data"
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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108 ---
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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109 <!--
22
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110 alphaFile: "test-data/alpha_levels.tabular"
26
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111 inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
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112 preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
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113 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
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114 regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$"
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115 regexSampleGrouping: "\\w+"
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116 groupFilterPatterns: ".+"
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117 groupFilter: !r c("none", "exclude", "include")[3]
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118 imputationMethod: !r c("group-median", "median", "mean", "random")[1]
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119 kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[1]
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120 ut_alphaFile: "test-data/alpha_levels.tabular"
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121 ut_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"
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122 ut_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"
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123 ut_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
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124 ut_regexSampleNames: "\\.\\d+[A-Z]$"
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125 ut_regexSampleGrouping: "\\d+"
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126 ut_groupFilterPatterns: ".+,.*"
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127 ut_groupFilter: !r c("none", "exclude", "include")[1]
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128 ut_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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129 ut_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1]
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130 tst_alphaFile: "test-data/alpha_levels.tabular"
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131 tst_inputFile: "test-data/test_input_for_anova.tabular"
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132 tst_preprocDb: "test-data/test_input_for_anova.sqlite"
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133 tst_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
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134 tst_regexSampleNames: "\\.\\d+[A-Z]$"
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135 tst_regexSampleGrouping: "\\d+"
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136 tst_groupFilterPatterns: ".+"
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137 tst_groupFilter: !r c("none", "exclude", "include")[1]
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138 tst_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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139 tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5]
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140
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141 tst_alphaFile: "test-data/alpha_levels.tabular"
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142 tst_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"
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143 tst_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"
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144 tst_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
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145 tst_regexSampleNames: "\\.\\d+[A-Z]$"
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146 tst_regexSampleGrouping: "\\d+"
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147 tst_groupFilterPatterns: ".+,.*"
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148 tst_groupFilter: !r c("none", "exclude", "include")[1]
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149 tst_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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150 tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5]
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151 px_alphaFile: "test-data/alpha_levels.tabular"
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152 px_inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
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153 px_preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
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154 px_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
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155 px_regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$"
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156 px_regexSampleGrouping: "\\w+"
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157 px_groupFilterPatterns: ".+"
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158 px_groupFilter: !r c("none", "exclude", "include")[3]
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159 px_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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160 px_kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5]
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161 pdx_alphaFile: "test-data/alpha_levels.tabular"
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162 pdx_inputFile: "test-data/PDX012970_pST.preproc_tab.tabular"
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163 pdx_preprocDb: "test-data/PDX012970_pST.preproc.sqlite"
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164 pdx_kseaAppPrepDb: !r c(":memory:", "test-data/PDX012970.sqlite")[2]
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165 pdx_regexSampleNames: "\\.\\w+\\.\\w+\\.\\d+[A-Z]$"
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166 pdx_regexSampleGrouping: "\\.\\w+\\K\\.\\w+"
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167 pdx_groupFilterPatterns: "AdCa,AVPC"
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168 pdx_groupFilter: !r c("none", "exclude", "include")[3]
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169 pdx_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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170 pdx_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1]
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171 tst_alphaFile: "test-data/alpha_levels.tabular"
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172 tst_inputFile: "test-data/test_input_for_anova.tabular"
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173 tst_preprocDb: "test-data/test_input_for_anova.sqlite"
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174 tst_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
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175 tst_regexSampleNames: "\\.\\d+[A-Z]$"
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176 tst_regexSampleGrouping: "\\d+"
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177 tst_groupFilterPatterns: ".+"
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178 tst_groupFilter: !r c("none", "exclude", "include")[1]
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179 tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5]
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180 tst_imputationMethod: !r c("group-median", "median", "mean", "random")[1]
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181 ut_alphaFile: "test-data/alpha_levels.tabular"
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182 ut_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"
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183 ut_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"
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184 ut_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
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185 ut_regexSampleNames: "\\.\\d+[A-Z]$"
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186 ut_regexSampleGrouping: "\\d+"
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187 ut_groupFilterPatterns: ".+,.*"
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188 ut_groupFilter: !r c("none", "exclude", "include")[1]
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189 ut_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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190 alphaFile: "test-data/alpha_levels.tabular"
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191 inputFile: "test-data/test_input_for_anova.tabular"
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192 preprocDb: "test-data/test_input_for_anova.sqlite"
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193 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
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194 regexSampleNames: "\\.\\d+[A-Z]$"
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195 regexSampleGrouping: "\\d+"
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196 groupFilterPatterns: ".+,.*"
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197 groupFilter: !r c("none", "exclude", "include")[1]
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198 imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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199 nd_alphaFile: "test-data/alpha_levels.tabular"
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200 nd_inputFile: "test-data/pST_Sites_NancyDu.txt.preproc.tabular"
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201 nd_preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"
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202 nd_kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]
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203 nd_regexSampleNames: "\\.\\d+[A-Z]$"
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204 nd_regexSampleGrouping: "\\d+"
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205 nd_groupFilterPatterns: ".+,.*"
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206 nd_groupFilter: !r c("none", "exclude", "include")[1]
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207 nd_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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208 pxd_alphaFile: "test-data/alpha_levels.tabular"
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209 pxd_inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
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210 pxd_preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
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211 pxd_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
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212 pxd_regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$"
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213 pxd_regexSampleGrouping: "\\w+"
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214 pxd_groupFilterPatterns: ".+"
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215 pxd_groupFilter: !r c("none", "exclude", "include")[3]
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216 pxd_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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217
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218 alphaFile: "test-data/alpha_levels.tabular"
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219 inputFile: "test-data/test_input_for_anova.tabular"
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220 preprocDb: "test-data/test_input_for_anova.sqlite"
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221 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
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222 regexSampleNames: "\\.\\d+[A-Z]$"
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223 regexSampleGrouping: "\\d+"
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224 groupFilterPatterns: ".+,.*"
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225 groupFilter: !r c("none", "exclude", "include")[1]
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226
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227 alphaFile: "test-data/alpha_levels.tabular"
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228 inputFile: "test-data/PDX012970_pST.preproc_tab.tabular"
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229 preprocDb: "test-data/PDX012970_pST.preproc.sqlite"
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230 kseaAppPrepDb: !r c(":memory:", "test-data/PDX012970.sqlite")[2]
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231 regexSampleNames: "\\.\\w+\\.\\w+\\.\\d+[A-Z]$"
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232 regexSampleGrouping: "\\.\\w+\\K\\.\\w+"
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233 groupFilterPatterns: "AdCa,AVPC"
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234 groupFilter: !r c("none", "exclude", "include")[3]
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235
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236 alphaFile: "test-data/alpha_levels.tabular"
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237 inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
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238 preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
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239 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
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240 regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$"
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241 regexSampleGrouping: "\\w+"
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242 groupFilterPatterns: ".+,.*"
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243 groupFilter: !r c("none", "exclude", "include")[3]
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244
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245 kseaCutoffStatistic: !r c("p.value", "FDR")[2]
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246 kseaCutoffThreshold: !r c(0.05, 0.1)[1]
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247
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248 alphaFile: "test-data/alpha_levels.tabular"
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249 inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"
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250 preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"
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251 kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
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252 regexSampleNames: "\\.\\d+[A-Z]$"
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253 regexSampleGrouping: "\\d+"
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254
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255 alphaFile: "test-data/alpha_levels.tabular"
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256 inputFile: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.tabular"
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257 preprocDb: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.sqlite"
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258 kseaAppPrepDb: !r c(":memory:", "test-data/pY_Sites_NancyDu.ksea.sqlite")[2]
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259 regexSampleNames: "\\.\\d+[A-Z]$"
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260 regexSampleGrouping: "\\d+"
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261 groupFilterPatterns: ".+,.*"
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262 groupFilter: !r c("none", "exclude", "include")[3]
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263
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264 alphaFile: "test-data/alpha_levels.tabular"
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265 inputFile: "test-data/pST_Sites_NancyDu.txt.preproc.tabular"
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266 preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"
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267 kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]
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268 regexSampleNames: "\\.\\d+[A-Z]$"
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269 regexSampleGrouping: "\\d+"
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270 groupFilterPatterns: ".+,.*"
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271 groupFilter: !r c("none", "exclude", "include")[1]
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272
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273 -->
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274 ```{r setup, include = FALSE, results = 'asis'}
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275
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276 # simple debug messaging
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277 print_nb_messages <- params$printNBMsgs
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278
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279 nb <- if (!print_nb_messages) {
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280 function(...) invisible()
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281 } else {
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282 function(..., f = cat) f("\n$\\exists{}\\supset\\forall{}$", ...)
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283 }
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284
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285 nbe <- if (!print_nb_messages) {
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286 function(...) invisible()
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287 } else {
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288 function(..., f = cat, file = stderr()) {
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289 cat(
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290 stringi::stri_unescape_unicode("\nNBE \\u2203\\u2283\\u2200"),
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291 ...,
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292 file = file
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293 )
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294 }
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295 }
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296
22
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297 #ref for debugging: https://yihui.org/tinytex/r/#debugging
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298 options(tinytex.verbose = TRUE)
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299
0
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300 # ref for parameterizing Rmd document: https://stackoverflow.com/a/37940285
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301 # ref for top and bottom struts: https://tex.stackexchange.com/a/50355
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302 knitr::opts_chunk$set(echo = FALSE, fig.dim = c(9, 10), dpi = 300)
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303
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304 # freeze the random number generator so the same results will be produced
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305 # from run to run
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306 set.seed(28571)
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307
22
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308 ### LIBRARIES
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309
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310 if (print_nb_messages) nbe("library(gplots)")
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311 library(gplots)
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312 if (print_nb_messages) nbe("library(caret)")
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313 # load caret for nearZeroVar
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314 if (print_nb_messages) nbe("Please ignore the messages about systemd, if any.\n")
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315 library(caret)
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316 if (print_nb_messages) nbe("library(DBI)")
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317 library(DBI)
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318 if (print_nb_messages) nbe("library(RSQLite)")
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319 library(RSQLite)
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320 if (print_nb_messages) nbe("library(sqldf)\n")
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321 # Suppress "Warning: no DISPLAY variable so Tk is not available"
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322 suppressWarnings(suppressMessages(library(sqldf)))
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323
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324 # required but not added to search list:
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325 # - DBI
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326 # - RSQLite
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327 # - ggplot2
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328 # - knitr
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329 # - latex2exp
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330 # - preprocessCore
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331 # - reshape2
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332 # - vioplot
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333
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334 ### CONSTANTS
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335
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336 const_boxplot_fill <- "grey94"
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337 const_ksea_astrsk_kinases <- 1
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338 const_ksea_nonastrsk_kinases <- 2
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339 const_ksea_all_kinases <- 3
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340 const_log10_e <- log10(exp(1))
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341 const_stripchart_cex <- 0.5
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342 const_stripchart_jitter <- 0.3
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343 const_table_anchor_bp <- "bp"
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344 const_table_anchor_ht <- "ht"
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345 const_table_anchor_p <- "p"
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346 const_table_anchor_t <- "t"
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347 const_table_anchor_tbp <- "tbp"
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348
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349
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350 ### GLOBAL VARIABLES (params)
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351
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352 ## functions to process params
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353
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354 is_string_null_or_empty <- function(x) {
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355 # N. B. non-strings are intentionally treated as NULL
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356 if (is.null(x))
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357 TRUE
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358 else if (!is.character(x))
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359 TRUE
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360 else x == ""
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361 }
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362
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363 ##' Catch *and* save both errors and warnings, and in the case of
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364 ##' a warning, also keep the computed result.
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365 ##' return result as list(value = ..., warning = ...)
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366 ##' - value will be:
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367 ##' - the result if no exception is thrown
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368 ##' - the exception if an exception is caught
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369 ##' - warning will be a string except perhaps when warning argument is not NULL
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370 ##'
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371 ##' adapted from `demo(error.catching)`
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372 ##'
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373 ##' @title tryCatch both warnings (with value) and errors
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374 ##' @param expr an \R expression to evaluate
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375 ##' @return a list with 'value' and 'warning', where
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376 ##' 'value' may be an error caught.
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377 ##' @author Martin Maechler;
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378 ##' Copyright (C) 2010-2012 The R Core Team
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379 try_catch_w_e <-
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380 function(expr, error = function(e) e, warning = NULL) {
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381 wrn <- NULL
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382 # warning handler
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383 w_handler <-
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384 if (is.function(warning))
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385 warning
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386 else
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387 function(w) {
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388 wrn <<- w
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389 invokeRestart("muffleWarning")
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390 }
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391 e_handler <-
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392 if (is.function(error))
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393 error
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394 else
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395 function(e) e
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396 # return result as list(value = ..., warning = ...)
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397 # - value will be:
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398 # - the result if no exception is thrown
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399 # - the exception if an exception is caught
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400 list(
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401 value = withCallingHandlers(
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diff changeset
402 tryCatch(
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diff changeset
403 expr,
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diff changeset
404 error = e_handler
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diff changeset
405 ),
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406 warning = w_handler
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diff changeset
407 ),
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408 warning = wrn
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diff changeset
409 )
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diff changeset
410 }
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diff changeset
411
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412 see_kvp <-
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diff changeset
413 function(format, key, value, suffix = "") {
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diff changeset
414 if (
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415 !all(
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416 is.character(format),
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417 is.character(key),
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418 is.character(value),
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419 is.character(suffix)
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420 )
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421 ) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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422 cat("all arguments to see_kvp should be character")
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423 knitr::knit_exit()
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424 }
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425 result <- sprintf(format, value)
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426 if (length(result) > 1) {
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427 sprintf(
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428 "%s = c(%s)%s",
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429 whack_underscores(key),
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430 paste(result, collapse = ", "),
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431 suffix
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432 )
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433 } else {
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434 sprintf(
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435 "%s = %s%s",
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diff changeset
436 key,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
437 result,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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438 suffix
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diff changeset
439 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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440 }
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diff changeset
441 }
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diff changeset
442
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diff changeset
443 see_logical <-
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444 function(x, suffix = "", xprssn = deparse1(substitute(x))) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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445 result <- as.character(as.logical(x))
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diff changeset
446 # handle NAs and NaNs
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447 result[is.na(result)] <- "NA"
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diff changeset
448 see_kvp(
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449 format = "%s",
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450 key = xprssn,
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diff changeset
451 value = result,
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diff changeset
452 suffix = suffix
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diff changeset
453 )
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diff changeset
454 }
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diff changeset
455
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diff changeset
456 see_numeric <-
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457 function(x, suffix = "", digits = 3, xprssn = deparse1(substitute(x))) {
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458 if (is.numeric(digits) && is.numeric(x)) {
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diff changeset
459 digits <- as.integer(digits)
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460 digits <- min(16, max(0, digits))
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461 format <- paste0("%0.", as.character(digits), "g")
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462 result <- sprintf(format, x)
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diff changeset
463 see_kvp(
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diff changeset
464 format = "%s",
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diff changeset
465 key = xprssn,
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diff changeset
466 value = result,
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diff changeset
467 suffix = suffix
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diff changeset
468 )
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diff changeset
469 }
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diff changeset
470 }
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diff changeset
471
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
472 see_character <-
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diff changeset
473 function(x, suffix = "", xprssn = deparse1(substitute(x))) {
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diff changeset
474 if (is.character(x)) {
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diff changeset
475 see_kvp(
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diff changeset
476 format = "%s",
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diff changeset
477 key = xprssn,
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diff changeset
478 value = sprintf("\"%s\"", x),
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diff changeset
479 suffix = suffix
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diff changeset
480 )
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diff changeset
481 }
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diff changeset
482 }
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diff changeset
483
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
484 see_variable <-
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diff changeset
485 function(x, suffix = "", digits = 3, xprssn = deparse1(substitute(x))) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
486 if (is.character(x)) {
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diff changeset
487 see_character(x, suffix, xprssn)
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488 } else if (is.numeric(x)) {
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diff changeset
489 see_numeric(x, suffix, digits, xprssn)
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490 } else if (is.logical(x)) {
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491 see_logical(x, suffix, xprssn)
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492 } else {
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493 f <- file("")
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494 sink(f)
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495 str(x)
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496 msg <- paste(readLines(f), collapse = "\n")
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497 sink()
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498 close(f)
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499 paste0(
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500 "see_variable - str(",
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501 xprssn,
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502 "):\n",
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503 msg, "\n"
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diff changeset
504 )
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505 }
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506 }
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507
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508 # ref: https://tug.org/texinfohtml/latex2e.html
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509 # LaTeX sets aside the following characters for special purposes.
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510 # For example, the percent sign % is for comments.
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511 # They are called reserved characters or special characters.
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512 # They are all discussed elsewhere in this manual.
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513 #
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514 # $ % & { } _ ~ ^ \ #
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515 #
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516 # If you want a reserved character to be printed as itself, in the text body
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517 # font, for all but the final three characters in that list simply put
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518 # a backslash \ in front of the character.
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519 # Thus, typing \$1.23 will produce $1.23 in your output.
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520 #
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521 # As to the last three characters, to get a tilde in the text body font,
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522 # use \~{} (omitting the curly braces would result in the next character
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523 # receiving a tilde accent).
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524 # Similarly, to get a text body font circumflex use \^{}.
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525 # To get a backslash in the font of the text body enter \textbackslash{}.
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526 whack_math <-
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527 function(v) {
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528 v <- as.character(v)
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529 w <- gsub("\\", "\\textbackslash ", v, fixed = TRUE)
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530 w <- Reduce(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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531 f = function(l, r) {
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532 gsub(r, paste0("\\", r), l, fixed = TRUE)
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533 },
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534 x = c("#", "$", "%", "&", "{", "}", "_"),
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535 init = w
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536 )
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537 w <- gsub("^", "\\^{}", w, fixed = TRUE)
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538 return(w)
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539 if (all(v == w))
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540 v
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diff changeset
541 else
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542 paste0("\\texttt{", w, "}")
22
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543 }
26
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544 whack_underscores <- whack_math
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diff changeset
545
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546 ## dump params to stderr (remove this eventually)
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diff changeset
547
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548 if (FALSE) nbe(see_variable(params))
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diff changeset
549
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diff changeset
550 ## unlist params for eventual output
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diff changeset
551
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552 param_unlist <- unlist(as.list(params))
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diff changeset
553
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554 # no need to whack underscores and dollars because this is verbatim
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555 param_df <- data.frame(
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556 parameter = paste0("\\verb@", names(param_unlist), "@"),
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557 value = paste0(
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558 "\n\\begin{tiny}\n\\verb@",
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diff changeset
559 param_unlist,
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diff changeset
560 "@\n\\end{tiny}"
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diff changeset
561 )
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diff changeset
562 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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563 param_df <- data.frame(
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564 parameter = names(param_unlist),
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565 value = param_unlist
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566 )
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567 param_df <- param_df[order(param_df$parameter), ]
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568
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569 ## general output control
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diff changeset
570
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571 debug_file_base_path <- params$debugFileBasePath
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572 print_trace_messages <- params$printTraceMsgs
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573 show_enriched_substrates <- params$showEnrichedSubstrates
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574 boxplot_varwidth <- params$boxPlotVarWidth
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575 boxplot_notch <- params$boxPlotNotch
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diff changeset
576
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diff changeset
577 ## parameters for static data
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diff changeset
578
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579 kinase_name_uprt_lut_bz2 <- params$kinaseNameUprtLutBz2
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580 kinase_uprt_desc_lut_bz2 <- params$kinaseUprtDescLutBz2
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581
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582 ## parameters for input file
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583
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584 preproc_db <- params$preprocDb
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585 alpha_file <- params$alphaFile
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586 input_file <- params$inputFile
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587
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588 # First data column - ideally, this could be detected via
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589 # regexSampleNames, but for now leave it as is.
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590 first_data_column <- params$firstDataColumn
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591 fdc_is_integer <- is.integer(first_data_column)
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592 if (fdc_is_integer) {
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593 first_data_column <- as.integer(params$firstDataColumn)
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594 }
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595
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596 ## parameters for output files
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597
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598 ksea_app_prep_db <- params$kseaAppPrepDb
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599 imputed_data_filename <- params$imputedDataFilename
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600 imp_qn_lt_data_filenm <- params$imputedQNLTDataFile
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601 anova_ksea_mtdt_file <- params$anovaKseaMetadata
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602
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603 ## parameters for imputation
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604
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605 # Imputation method, should be one of
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606 # "random", "group-median", "median", or "mean"
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607 imputation_method <- params$imputationMethod
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608
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609 # Selection of percentile of logvalue data to set the mean for random number
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610 # generation when using random imputation
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611 mean_percentile <- params$meanPercentile / 100.0
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612
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613 # deviation adjustment-factor for random values; real number.
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614 sd_percentile <- params$sdPercentile
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615
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616 ## parameters for group parsing and filtering
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617
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618 # Regular expression of Sample Names, e.g., "\\.(\\d+)[A-Z]$"
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619 regex_sample_names <- params$regexSampleNames
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620 # Regular expression to extract Sample Grouping from Sample Name;
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621 # if error occurs, compare smpl_trt vs. sample_name_matches
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622 # to see if groupings/pairs line up
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623 # e.g., "(\\d+)"
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624
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625 regex_sample_grouping <- params$regexSampleGrouping
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626 # What are the patterns for filtering sample groups?
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627 # How should sample groups be filtered?
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628 # - none: do not filter
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629 # - include: include sample groups matching filter
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630 # - exclude: include sample groups not matching filter
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631
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632 sample_group_filter <- params$groupFilter
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633 if (grepl("f", params$groupFilterMode, fixed = TRUE)) {
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634 sample_group_filter_perl <- FALSE
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635 sample_group_filter_fixed <- TRUE
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636 } else if (grepl("p", params$groupFilterMode, fixed = TRUE)) {
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637 sample_group_filter_perl <- TRUE
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638 sample_group_filter_fixed <- FALSE
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639 } else { # normal regex
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640 sample_group_filter_perl <- FALSE
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641 sample_group_filter_fixed <- FALSE
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642 }
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643
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644 sample_group_filter_nocase <-
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645 grepl("i", params$groupFilterMode, fixed = TRUE)
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646
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647 # What PCRE patterns should be included or excluded
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648 group_filter_patterns_csv <- params$groupFilterPatterns
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649 sample_group_filter_patterns <- strsplit(
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650 x = group_filter_patterns_csv,
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651 split = ",",
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652 fixed = TRUE
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653 )[[1]]
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654
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655 ## parameters for hypothesis testing
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656
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657 one_way_all_categories_fname <- params$oneWayManyCategories
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658
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659 one_way_all_categories <- try_catch_w_e(
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660 match.fun(one_way_all_categories_fname))
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661
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662 if (!is.function(one_way_all_categories$value)) {
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663 write("fatal error for parameter oneWayManyCategories:", stderr())
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diff changeset
664 write(one_way_all_categories$value$message, stderr())
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
665 if (sys.nframe() > 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
666 cat("Cannot continue and quit() failed. Goodbye.")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
667 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
668 quit(save = "no", status = 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
669 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
670 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
671
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
672 one_way_all_categories <- one_way_all_categories$value
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
673
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
674 one_way_two_categories_fname <- params$oneWayManyCategories
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
675 one_way_two_categories <- try_catch_w_e(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
676 match.fun(one_way_two_categories_fname))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
677 if (!is.function(one_way_two_categories$value)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
678 cat("fatal error for parameter oneWayTwoCategories: \n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
679 cat(one_way_two_categories$value$message, fill = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
680 if (sys.nframe() > 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
681 cat("Cannot continue and quit() failed. Goodbye.")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
682 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
683 quit(save = "no", status = 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
684 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
685 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
686 one_way_two_categories <- one_way_two_categories$value
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
687
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
688 ## parameters for KSEA
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
689
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
690 ksea_cutoff_statistic <- params$kseaCutoffStatistic
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
691 ksea_cutoff_threshold <- params$kseaCutoffThreshold
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
692 ksea_min_substrate_count <- params$kseaMinSubstrateCount
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
693
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
694 ## parameters for global variables consumed by functions
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
695
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
696 # intensityHeatmapCriteria: !r c("na_count", "p_value")[2] # TODO switch to 1
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
697 # TODO Validate within list
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
698 g_intensity_hm_criteria <- params$intensityHeatmapCriteria
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
699 if (is_string_null_or_empty(g_intensity_hm_criteria)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
700 cat("invalid intensityHeatmapCriteria parameter (must be string)")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
701 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
702 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
703 switch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
704 g_intensity_hm_criteria,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
705 "quality" = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
706 "na_count" = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
707 "p_value" = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
708 {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
709 with(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
710 params,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
711 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
712 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
713 "invalid %s (must be %s)",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
714 see_variable(intensityHeatmapCriteria),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
715 "one of quality or na_count or p_value"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
716 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
717 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
718 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
719 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
720 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
721 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
722
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
723 # intensityHeatmapRows: 50
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
724 # TODO Validate >> 0 < 75
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
725 g_intensity_hm_rows <- params$intensityHeatmapRows
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
726 if (!is.integer(g_intensity_hm_rows) || g_intensity_hm_rows < 1) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
727 cat("invalid intensityHeatmapRows (must be integer > 0)")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
728 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
729 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
730
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
731 g_intensity_min_per_class <- params$intensityMinValuesPerGroup
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
732 if (!is.integer(g_intensity_min_per_class) || g_intensity_min_per_class < 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
733 cat("invalid intensityMinValuesPerGroup (must be integer > -1")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
734 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
735 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
736
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
737 if (is.na(as.logical(g_correlate_substrates <- params$correlateSubstrates))) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
738 cat("invalid correlateSubstrates (must be TRUE or FALSE)")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
739 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
740 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
741
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
742 if (is.na(as.logical(g_filter_cov_var_gt_1 <- params$filterCovVarGT1))) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
743 cat("invalid filterCovVarGT1 parameter (must be TRUE or FALSE)")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
744 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
745 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
746
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
747 # TODO Validate >> 0 < 30
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
748 g_ppep_trunc_n <- params$ppepTruncN
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
749
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
750 # TODO Validate >> 0 < 30
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diff changeset
751 g_subgene_trunc_n <- params$subgeneTruncN
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
752
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
753 # TODO Validate >> 0 < 30
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diff changeset
754 g_sbstr_trunc_n <- params$substTruncN
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
755
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
756
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
757 ### OPERATORS
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
758
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
759 # Test for exclusion
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
760 # ref: https://www.reneshbedre.com/blog/in-operator-r.html
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
761 `%notin%` <- Negate(`%in%`)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
762
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
763 # Augmented assignment
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
764 # ref: https://www2.cs.arizona.edu/icon/refernce/infix2.htm#aug_assign
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
765 `%||:=%` <- function(lvalue, ...) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
766 pf <- parent.frame()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
767 rvalue <- Reduce(paste0, x = ..., init = lvalue)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
768 assign(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
769 x = as.character(substitute(lvalue)),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
770 value = rvalue,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
771 pos = pf
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
772 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
773 invisible(rvalue)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
774 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
775
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
776 ### FUNCTIONS
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
777
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
778 no_op <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
779 function() {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
780 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
781 # this function is not used in this file and should be removed while
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
782 # factoring out reusable code
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
783 all_apply <- function(f, v, na_rm = TRUE, ...) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
784 Reduce(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
785 f = function(l, r) if (na_rm && is.na(r)) TRUE else l && r,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
786 x = sapply(X = v, FUN = f, ...),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
787 init = TRUE
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
788 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
789 }
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
790
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
791 write_debug_file <- function(data_frame) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
792 if (!is.null(debug_file_base_path)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
793 s_path <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
794 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
795 "%s/%s.txt",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
796 debug_file_base_path,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
797 deparse(substitute(data_frame))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
798 )
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
799 write.table(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
800 data_frame,
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
801 file = s_path,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
802 sep = "\t",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
803 col.names = TRUE,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
804 row.names = TRUE,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
805 quote = FALSE
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
806 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
807 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
808 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
809
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
810 # ref: http://adv-r.had.co.nz/Environments.html
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
811 # "When creating your own environment, note that you should set its parent
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
812 # environment to be the empty environment. This ensures you don't
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
813 # accidentally inherit objects from somewhere else."
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
814 # Caution: this prevents `with(my_env, expr)` from working when `expr`
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
815 # contains anything from the global environment, even operators!
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
816 # Hence, `x <- 1; get("x", new_env())` fails by design.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
817 new_env <- function() {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
818 new.env(parent = emptyenv())
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
819 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
820
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
821 # make apply readable for rows
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
822 row_apply <- function(x, fun, ..., simplify = TRUE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
823 apply(x, MARGIN = 1, fun, ..., simplify = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
824 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
825
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
826 # make apply readable for columns
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
827 column_apply <- function(x, fun, ..., simplify = TRUE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
828 apply(x, MARGIN = 2, fun, ..., simplify = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
829 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
830
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
831 ##' Produce a vector of boolean values whose i-th value is TRUE when any
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
832 ##' member of v matches the i-th membr of s, where i in 1:seq_len(length(s))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
833 ##'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
834 ##' @title Search multiple strings for matches of multiple substrings
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
835 ##' @param v a vector of substrings to match
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
836 ##' @param s a vector of strings to search for matches
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
837 ##' @param ... additional arguments to grepl
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
838 ##' @return a list with keys in s and valuse that are vectors of elements of v
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
839 ##' @author Art Eschenlauer
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
840 ##' Copyright (C) 2022 Art Eschenlauer;
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
841 ##' MIT License; https://en.wikipedia.org/wiki/MIT_License#License_terms
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
842 mgrepl <- function(v, s, ...) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
843 grpl_rslt <- rep_len(0, length(s))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
844 for (vi in v) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
845 grpl_rslt_v <- sapply(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
846 X = s,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
847 FUN = function(t) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
848 Reduce(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
849 f = function(l, r) if (is.null(l)) r else c(l, r),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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850 x = sapply(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
851 X = vi,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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852 FUN = function(f) grepl(f, t, ...)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
853 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
854 init = c()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
855 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
856 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
857 simplify = "array"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
858 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
859 grpl_rslt <- grpl_rslt + grpl_rslt_v
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
860 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
861 rslt <- unname(grpl_rslt > 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
862 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
863
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
864 ##' Produce positions in a vector where succeeding value != current valus
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
865 ##'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
866 ##' @title Search vector for neighboring positions having different values
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
867 ##' @param v a vector of comparable numeric values (e.g. integers)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
868 ##' @return a vector of positions i where v[i] != v[i + 1]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
869 ##' @author Art Eschenlauer
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
870 ##' Copyright (C) 2022 Art Eschenlauer;
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
871 ##' MIT License; https://en.wikipedia.org/wiki/MIT_License#License_terms
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
872 transition_positions <- function(v) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
873 Reduce(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
874 f = function(l, i) if ((i != 1) && (v[i - 1] != v[i])) c(l, i - 1) else l,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
875 x = seq_along(v)[-1:0],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
876 init = c()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
877 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
878 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
879
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
880 ### figure debug functions
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
881
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
882 cat_par_vector <- function(par_name, lbl = "", newlines = TRUE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
883 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
884 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
885 "%spar(%s) = c(%s)%s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
886 lbl,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
887 par_name,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
888 paste(par(par_name), collapse = ", "),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
889 if (newlines) "\n\n" else ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
890 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
891 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
892 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
893
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
894 cat_margins <- function(lbl = NULL) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
895 for (p in c("fig", "fin", "mar", "mai", "omd", "omi", "oma"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
896 cat_par_vector(p, if (!is.null(lbl)) paste0(lbl, " ") else NULL)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
897 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
898
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
899 cat_variable <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
900 function(x, suffix = "", digits = 3, force_str = FALSE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
901 xprssn <- deparse1(substitute(x))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
902 if (force_str || is.matrix(x) || is.list(x) || is.data.frame(x)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
903 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
904 paste0(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
905 "\n\\texttt{\\textbf{",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
906 whack_underscores(xprssn),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
907 "}} [",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
908 typeof(x),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
909 ",",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
910 mode(x),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
911 "] =\n"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
912 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
913 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
914 cat("\n\\begin{verbatim}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
915 str(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
916 cat("\n\\end{verbatim}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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917 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
918 cat("\n", see_variable(x, suffix, digits, xprssn))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
919 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
920 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
921
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
922 ### structure helper functions
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
923
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
924 # ref: staque.R - Icon-oriented stack and queue operations
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
925 # - https://gist.github.com/eschen42/917690355e53918b9e7ba7138a02d1f8
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
926 #
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
927 # sq_get(v):x produces the leftmost element of v and removes it from v,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
928 # but produces NA if v is empty
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
929 sq_get <- function(v) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
930 if (length(v) == 0) return(NA)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
931 assign(as.character(substitute(v)), v[-1], parent.frame())
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
932 return(v[1])
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
933 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
934 #
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
935 # sq_put(v,x1,...,xn):v puts x1, x2, ..., xn onto the right end of v,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
936 # producing v.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
937 # Values are pushed in order from left to right,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
938 # so xn becomes the last (rightmost) value on v.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
939 # sq_put(v) with no second argument does nothing.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
940 sq_put <- function(v, x = NA, ...) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
941 pf <- parent.frame()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
942 if (is.null(x)) return(pf$v)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
943 if (
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
944 !(length(x) > 1) &&
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
945 !rlang::is_closure(x) &&
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
946 is.na(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
947 ) return(pf$v)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
948 assign(as.character(substitute(v)), c(v, x, ...), pf)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
949 pf[[as.character(substitute(v))]]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
950 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
951
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
952 ### numerical/statistical helper functions
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
953
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
954 any_nan <- function(x) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
955 !any(x == "NaN")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
956 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
957
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
958 # determine standard deviation of quantile to impute
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
959 sd_finite <- function(x) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
960 ok <- is.finite(x)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
961 sd(x[ok])
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
962 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
963
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
964 # compute anova raw p-value
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
965 anova_func <- function(x, grouping_factor, one_way_f) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
966 subject <- data.frame(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
967 intensity = x
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
968 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
969 x_aov <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
970 one_way_f(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
971 formula = intensity ~ grouping_factor,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
972 data = subject
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
973 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
974 pvalue <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
975 if (identical(one_way_f, aov))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
976 summary(x_aov)[[1]][["Pr(>F)"]][1]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
977 else
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
978 pvalue <- x_aov$p.value
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
979 pvalue
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
980 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
981
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
982 # This code adapted from matrixcalc::is.positive.definite
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
983 # Notably, this simply tests without calling stop()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
984 is_positive_definite <- function(x, tol = 1e-08) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
985 if (!is.matrix(x))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
986 return(FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
987 if (!is.numeric(x))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
988 return(FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
989 if (nrow(x) < 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
990 return(FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
991 if (ncol(x) < 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
992 return(FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
993 if (nrow(x) != ncol(x))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
994 return(FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
995 sum_symm <- sum(x == t(x), na.rm = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
996 value_count <- Reduce("*", dim(x))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
997 if (sum_symm != value_count)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
998 return(FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
999 eigenvalues <- eigen(x, only.values = TRUE)$values
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1000 n <- nrow(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1001 for (i in 1:n) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1002 if (abs(eigenvalues[i]) < tol) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1003 eigenvalues[i] <- 0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1004 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1005 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1006 if (any(eigenvalues <= 0)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1007 return(FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1008 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1009 return(TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1010 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1011
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1012 ### LaTeX functions
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1013
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1014 # Use this like print.data.frame, from which it is adapted:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1015 data_frame_table_latex <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1016 function(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1017 x,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1018 # digits to pass to format.data.frame
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1019 digits = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1020 # TRUE -> right-justify columns; FALSE -> left-justify
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1021 right = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1022 # maximumn number of rows to print
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1023 max = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1024 # string with justification of each column
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1025 justification = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1026 # TRUE to center on page
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1027 centered = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1028 # optional caption
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1029 caption = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1030 # h(inline); b(bottom); t (top) or p (separate page)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1031 anchor = "h",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1032 # set underscore_whack to TRUE to escape underscores
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1033 underscore_whack = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1034 # how to emit results
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1035 emit = cat
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1036 ) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1037 if (is.null(justification))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1038 justification <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1039 Reduce(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1040 f = paste,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1041 x = rep_len(if (right) "r" else "l", length(colnames(x)))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1042 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1043 n <- length(rownames(x))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1044 if (length(x) == 0L) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1045 emit(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1046 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1047 # if n is one, use singular 'row', else use plural 'rows'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1048 ngettext(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1049 n,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1050 "data frame with 0 columns and %d row",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1051 "data frame with 0 columns and %d rows"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1052 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1053 n
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1054 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1055 "\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1056 sep = ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1057 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1058 } else if (n == 0L) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1059 emit("0 rows for:\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1060 latex_itemized_list(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1061 v = names(x),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1062 underscore_whack = underscore_whack
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1063 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1064 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1065 if (is.null(max))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1066 max <- getOption("max.print", 99999L)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1067 if (!is.finite(max)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1068 cat("Abend because: invalid 'max' / getOption(\"max.print\"): ", max)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1069 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1070 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1071 omit <- (n0 <- max %/% length(x)) < n
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1072 m <- as.matrix(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1073 format.data.frame(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1074 if (omit) x[seq_len(n0), , drop = FALSE] else x,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1075 digits = digits,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1076 na.encode = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1077 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1078 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1079 emit(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1080 # h(inline); b(bottom); t (top) or p (separate page)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1081 paste0("\\begin{table}[", anchor, "]"),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1082 "\\leavevmode",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1083 sep = "\n"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1084 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1085 if (!is.null(caption))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1086 emit(paste0(" \\caption{", caption, "}"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1087 if (centered) emit("\\centering\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1088 emit(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1089 paste(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1090 " \\begin{tabular}{",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1091 justification,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1092 "}\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1093 sep = ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1094 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1095 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1096
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1097 # ref for top and bottom struts (\T and \B):
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1098 # https://tex.stackexchange.com/a/50355
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1099 if (!is.null(caption))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1100 emit("\\B \\\\\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1101 latex_table_row(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1102 v = colnames(m),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1103 extra = " \\T \\B",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1104 underscore_whack = underscore_whack
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1105 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1106 emit("\\hline \\\\\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1107 for (i in seq_len(length(m[, 1]))) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1108 latex_table_row(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1109 v = m[i, ],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1110 underscore_whack = underscore_whack
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1111 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1112 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1113 emit(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1114 paste(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1115 " \\end{tabular}",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1116 "\\end{table}",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1117 sep = "\n"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1118 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1119 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1120 if (omit)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1121 emit(" [ reached 'max' / getOption(\"max.print\") -- omitted",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1122 n - n0, "rows ]\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1123 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1124 invisible(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1125 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1126
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1127 # Use this like print.data.frame, from which it is adapted:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1128 data_frame_tabbing_latex <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1129 function(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1130 x,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1131 # vector of tab stops, in inches
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1132 tabstops,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1133 # vector of headings, registered with tab-stops
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1134 headings = colnames(x),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1135 # digits to pass to format.data.frame
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1136 digits = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1137 # maximumn number of rows to print
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1138 max = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1139 # optional caption
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1140 caption = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1141 # set underscore_whack to TRUE to escape underscores
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1142 underscore_whack = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1143 # flag for landscape mode
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1144 landscape = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1145 # flag indicating that subsubsection should be used for caption
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1146 # rather than subsection
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1147 use_subsubsection_header = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1148 # character-size indicator; for possible values, see:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1149 # https://tug.org/texinfohtml/latex2e.html#Font-sizes
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1150 charactersize = "small",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1151 # set verbatim to TRUE to debug output
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1152 verbatim = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1153 ) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1154
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1155 hlinport <- if (landscape) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1156 function() cat("\\hlinlscp \\\\\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1157 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1158 function() cat("\\hlinport \\\\\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1159 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1160
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1161 tabstops_tex <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1162 Reduce(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1163 f = function(l, r) paste0(l, r),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1164 x = sprintf("\\hspace{%0.2fin}\\=", tabstops),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1165 init = ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1166 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1167
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1168 n <- length(rownames(x))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1169 if (length(x) == 0L) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1170 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1171 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1172 # if n is one, use singular 'row', else use plural 'rows'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1173 ngettext(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1174 n,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1175 "data frame with 0 columns and %d row",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1176 "data frame with 0 columns and %d rows"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1177 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1178 n
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1179 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1180 "\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1181 sep = ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1182 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1183 } else if (n == 0L) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1184 cat("0 rows for:\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1185 latex_itemized_list(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1186 v = names(x),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1187 underscore_whack = underscore_whack
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1188 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1189 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1190 if (is.null(max))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1191 max <- getOption("max.print", 99999L)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1192 if (!is.finite(max)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1193 cat("Abend because: invalid 'max' / getOption(\"max.print\"): ", max)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1194 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1195 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1196 omit <- (n0 <- max %/% length(x)) < n
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1197 m <- as.matrix(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1198 format.data.frame(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1199 if (omit) x[seq_len(n0), , drop = FALSE] else x,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1200 digits = digits,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1201 na.encode = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1202 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1203 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1204 if (landscape)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1205 cat("\n\\begin{landscape}")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1206 tex_caption <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1207 if (!is.null(caption)) sprintf("\\captionof{table}{%s}\n", caption)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1208 else "\n"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1209 # build the column names, which have multiple lines when
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1210 # length(headings) is a multiple of the number of columns
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1211 column_names <- ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1212 while (length(headings) > 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1213 my_row <- c()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1214 for (i in 1:(1 + length(tabstops))) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1215 my_field <- sq_get(headings)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1216 sq_put(my_row, if (is.na(my_field)) "" else my_field)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1217 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1218 column_names %||:=% latex_tabbing_row(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1219 v = my_row,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1220 underscore_whack = underscore_whack,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1221 action = paste0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1222 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1223 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1224
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1225 # Begin tabbing environment after beginning charactersize environment
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1226 if (verbatim) cat("\n\\begin{verbatim}")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1227 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1228 paste0(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1229 "\n\\begin{", charactersize, "}", tex_caption,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1230 "\\begin{tabwrap}{", tabstops_tex, "}\n"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1231 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1232 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1233 # emit column names
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1234 cat(column_names)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1235 # emit hline
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1236 hlinport()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1237 for (i in seq_len(length(m[, 1]))) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1238 my_row <- latex_tabbing_row(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1239 v = m[i, ],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1240 underscore_whack = underscore_whack,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1241 action = paste0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1242 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1243 if (FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1244 cat(my_row)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1245 else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1246 cat(my_row)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1247 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1248 hlinport()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1249 if (omit)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1250 cat(" [ reached 'max' / getOption(\"max.print\") -- omitted",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1251 n - n0, "rows ]\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1252 # End charactersize environment after ending tabbing environment
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1253 cat(paste0("\\end{tabwrap}\n\\end{", charactersize, "}\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1254 if (verbatim) cat("\\end{verbatim}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1255 if (landscape)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1256 cat("\\end{landscape}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1257 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1258 invisible(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1259 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1260
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1261 param_df_noexit <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1262 function(e = NULL) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1263 data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1264 x = param_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1265 tabstops = c(1.75),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1266 underscore_whack = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1267 caption = "Input parameters",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
1268 verbatim = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1269 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1270 if (!is.null(e)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1271 sink(stderr())
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1272 cat("Caught fatal error:\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1273 str(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1274 sink()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1275 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1276 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1277
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1278 param_df_exit <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1279 function(e = NULL) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1280 param_df_noexit(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1281 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1282 exit(-1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1283 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1284
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1285 # exit with exit code (default 0) and optional msg
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1286 exit <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1287 function(code = 0, msg = NULL, use_stderr = FALSE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1288 if (!is.null(msg)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1289 if (use_stderr) sink(stderr())
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1290 cat("\n\n", msg, "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1291 if (use_stderr) sink()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1292 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1293 q(save = "no", status = code)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1294 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1295
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1296 # make control sequences into printable latex sequences
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1297 latex_printable_control_seqs <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1298 function(s) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1299 s <- gsub("[\\]", "xyzzy_plugh", s)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1300 s <- gsub("[$]", "\\\\$", s)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1301 s <- gsub("xyzzy_plugh", "$\\\\backslash$", s)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1302 return(s)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1303 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1304 nolatex_verbatim <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1305 function(expr) eval(expr)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1306
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1307 latex_verbatim <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1308 function(expr) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1309 arg_string <- deparse1(substitute(expr))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1310 cat("\n\\begin{verbatim}\n___\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1311 tryCatch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1312 expr = expr,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1313 error = param_df_exit,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1314 #ACE error =
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1315 #ACE function(e) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1316 #ACE cat("Caught error:\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1317 #ACE str(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1318 #ACE knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1319 #ACE stop(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1320 #ACE },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1321 finally = cat("...\n\\end{verbatim}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1322 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1323 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1324
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1325 latex_samepage <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1326 function(expr) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1327 arg_string <- deparse1(substitute(expr))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1328 cat("\n\\begin{samepage}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1329 tryCatch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1330 expr = expr,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1331 error = param_df_exit,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1332 #ACE error =
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1333 #ACE function(e) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1334 #ACE cat("Caught error:\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1335 #ACE str(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1336 #ACE knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1337 #ACE stop(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1338 #ACE },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1339 finally = cat("\n\\end{samepage}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1340 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1341 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1342
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1343 # return the result of invocation after showing parameters
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1344 # ref: https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1345 latex_show_invocation <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1346 function(f, f_name = deparse1(substitute(f)), head_patch = FALSE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1347 function(...) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1348 my_env <- (as.list(environment()))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1349 va <- list(...)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1350 my_rslt <- new_env()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1351 my_rslt$rslt <- NULL
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1352 latex_verbatim(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1353 expr = {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1354 cat(sprintf("\n .. Local variables for '%s':\n\n", f_name))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1355 str(va)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1356 if (!head_patch) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1357 # return this result
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1358 # ref: https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1359 cat(sprintf("\n .. Invoking '%s'\n", f_name))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1360 tryCatch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1361 {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1362 cat("\n\\end{verbatim}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1363 rslt <- do.call(f, va)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1364 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1365 error = param_df_exit,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1366 #ACE error = function(e) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1367 #ACE cat("\n\\begin{verbatim}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1368 #ACE str(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1369 #ACE cat("\n\\end{verbatim}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1370 #ACE knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1371 #ACE stop(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1372 #ACE },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1373 finally = cat("\n\\begin{verbatim}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1374 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1375 cat(sprintf("\n .. '%s' returned:\n", f_name))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1376 str(rslt)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1377 my_rslt$rslt <- rslt
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1378 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1379 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1380 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1381 # return the result of invocation with the shown parameters
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1382 # ref: https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1383 if (head_patch) my_rslt$rslt <- do.call(f, va)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1384 (my_rslt$rslt)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1385 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1386 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1387
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1388 latex_collapsed_vector <- function(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1389 collapse_string,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1390 v,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1391 underscore_whack = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1392 action = cat0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1393 ) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1394 v_sub <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1395 if (underscore_whack) whack_underscores(v) else v
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1396 action(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
1397 paste0(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1398 v_sub,
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
1399 collapse = collapse_string
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1400 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1401 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1402 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1403
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1404 latex_itemized_collapsed <- function(collapse_string, v, underscore_whack = TRUE) {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
1405 cat("\\begin{itemize}\n\\item ")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1406 latex_collapsed_vector(collapse_string, v, underscore_whack)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
1407 cat("\n\\end{itemize}\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1408 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1409
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1410 latex_itemized_list <- function(v, underscore_whack = TRUE) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1411 latex_itemized_collapsed("\n\\item ", v, underscore_whack)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1412 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1413
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1414 latex_enumerated_collapsed <- function(collapse_string, v, underscore_whack = TRUE) {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1415 cat("\\begin{enumerate}\n\\item ")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1416 latex_collapsed_vector(collapse_string, v, underscore_whack)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1417 cat("\n\\end{enumerate}\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1418 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1419
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1420 latex_enumerated_list <- function(v) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
1421 latex_enumerated_collapsed("\n\\item ", v)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1422 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1423
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1424 latex_table_row <- function(v, extra = "", underscore_whack = TRUE) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1425 latex_collapsed_vector(" & ", v, underscore_whack)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1426 cat(extra)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1427 cat(" \\\\\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1428 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1429
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1430 latex_tabbing_row <- function(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1431 v,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1432 extra = "",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1433 underscore_whack = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1434 action = cat0
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1435 ) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1436 # latex_collapsed_vector applies action to result of paste0;
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1437 # by default, action = cat;
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1438 # hence, a scalar string is assigned to v_collapsed
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1439 v_collapsed <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1440 latex_collapsed_vector(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1441 "} \\> \\tabfill{",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1442 v,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1443 underscore_whack,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1444 action = paste0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1445 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1446 action(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1447 "\\tabfill{",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1448 v_collapsed,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1449 "}",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1450 extra,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1451 " \\\\\n"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1452 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1453 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1454
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1455 # N.B. use con = "" to emulate regular cat
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1456 fcat0 <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1457 function(..., sprtr = " ", cnnctn = file()) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1458 cat0(..., sep = sprtr, file = cnnctn)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1459 invisible(cnnctn)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1460 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1461
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1462 hypersub <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1463 function(s) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1464 hyper <- tolower(s)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1465 hyper <- gsub("[^a-z0-9]+", "-", hyper)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1466 hyper <- gsub("[-]+", "-", hyper)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1467 hyper <- gsub("[_]+", "-", hyper)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1468 hyper <- sub("^[-]", "", hyper)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1469 hyper <- sub("[-]$", "", hyper)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1470 return(hyper)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1471 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1472
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1473 table_href <- function(s = "offset", caption = "") {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1474 paste0("\\hyperlink{table.\\arabic{", s, "}}{Table \\arabic{", s, "}}")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1475 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1476
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1477 table_offset <- function(i = 0, s = "offset", new = FALSE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1478 paste0(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1479 if (new) paste0("\\newcounter{", s, "}\n") else "",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1480 "\\setcounter{", s, "}{\\value{table}}\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1481 paste0(if (i > 0) rep(paste0("\\stepcounter{", s, "}"), i), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1482 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1483 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1484
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1485 a_section_header <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1486 function(s, prefix = "") {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1487 hyper <- hypersub(s)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1488 my_subsection_header <- sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1489 "\\hypertarget{%s}{\\%ssection{%s}\\label{%s}}\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1490 hyper,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1491 prefix,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1492 gsub("_", "\\_", s, fixed = TRUE),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1493 hyper
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1494 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1495 my_subsection_header
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1496 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1497 section_header <- function(s) a_section_header(s, "")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1498 subsection_header <- function(s) a_section_header(s, "sub")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
1499 subsubsection_header <- function(s) a_section_header(s, "subsub")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1500
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1501 ### SQLite functions
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1502
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1503 ddl_exec <- function(db, sql) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1504 discard <- DBI::dbExecute(conn = db, statement = sql)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1505 if (FALSE && discard != 0) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1506 need_newpage <- TRUE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1507 if (need_newpage) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1508 need_newpage <<- FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1509 cat("\\newpage\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1510 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1511 o_file <- stdout()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1512 cat("\n\\begin{verbatim}\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1513 cat(sql, file = o_file)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1514 cat(sprintf("\n%d rows affected by DDL\n", discard), file = o_file)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1515 cat("\n\\end{verbatim}\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1516 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1517 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1518
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1519 dml_no_rows_exec <- function(db, sql) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1520 discard <- DBI::dbExecute(conn = db, statement = sql)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1521 if (discard != 0) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1522 need_newpage <- TRUE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1523 if (need_newpage) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1524 need_newpage <<- FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1525 cat("\\newpage\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1526 }
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diff changeset
1527 cat("\n\\begin{verbatim}\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1528 o_file <- stdout()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1529 cat(sql, file = o_file)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1530 cat(sprintf("\n%d rows affected by DML\n", discard), file = o_file)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1531 cat("\n\\end{verbatim}\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1532 }
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diff changeset
1533 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1534
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1535 ### KSEA functions and helpers
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1536
26
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diff changeset
1537 #' The KSEA App Analysis (KSEA Kinase Scores Only)
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diff changeset
1538 #'
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diff changeset
1539 #' Compute KSEA kinase scores and statistics from phoshoproteomics data input
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diff changeset
1540 #' Adapted from KSEAapp::KSEA.Scores to allow retrieval of maximum log2(FC)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1541 #'
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diff changeset
1542 #' Result is an R data.frame with column names
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1543 #' "Kinase.Gene", "mS", "Enrichment", "m", "z.score", "p.value", "FDR"
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diff changeset
1544 #' "Please refer to the original Casado et al. publication for detailed
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1545 #' description of these columns and what they represent:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1546 #'
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diff changeset
1547 #' - Kinase.Gene indicates the gene name for each kinase.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1548 #' - mS represents the mean log2(fold change) of all the
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1549 #' kinase's substrates.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1550 #' - Enrichment is the background-adjusted value of the kinase's mS.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1551 #' - m is the total number of detected substrates
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1552 #' from the experimental dataset for each kinase.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1553 #' - z.score is the normalized score for each kinase, weighted by
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1554 #' the number of identified substrates.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1555 #' - p.value represents the statistical assessment for the z.score.
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diff changeset
1556 #' - FDR is the p-value adjusted for multiple hypothesis testing
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diff changeset
1557 #' using the Benjamini & Hochberg method."
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diff changeset
1558 #'
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diff changeset
1559 #' @param ksdata the Kinase-Substrate dataset uploaded from the file
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diff changeset
1560 #' prefaced with "PSP&NetworKIN_"
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diff changeset
1561 #' available from github.com/casecpb/KSEA/
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diff changeset
1562 #' @param px the experimental data file formatted as described in
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diff changeset
1563 #' the KSEA.Complete() documentation
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1564 #' @param networkin a binary input of TRUE or FALSE, indicating whether
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1565 #' or not to include NetworKIN predictions, where
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1566 #' \code{NetworKIN = TRUE}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1567 #' means include NetworKIN predictions
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1568 #' @param networkin_cutoff a numeric value between 1 and infinity setting
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1569 #' the minimum NetworKIN score
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1570 #' (this can be omitted if NetworKIN = FALSE)
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diff changeset
1571 #'
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diff changeset
1572 #' @return creates a new R data.frame with all the KSEA kinase
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1573 #' scores, along with each one's statistical
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1574 #' assessment, as described herein.
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diff changeset
1575 #'
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diff changeset
1576 #' @references
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diff changeset
1577 #'
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diff changeset
1578 #' Casado et al. (2013) Sci Signal. 6(268):rs6
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diff changeset
1579 #'
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diff changeset
1580 #' Hornbeck et al. (2015) Nucleic Acids Res. 43:D512-20
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diff changeset
1581 #'
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diff changeset
1582 #' Horn et al. (2014) Nature Methods 11(6):603-4
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diff changeset
1583 #'
22
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diff changeset
1584 ksea_scores <- function(
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diff changeset
1585 # For human data, typically, ksdata = KSEAapp::ksdata
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diff changeset
1586 ksdata,
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diff changeset
1587
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diff changeset
1588 # Input data file having columns:
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1589 # - Protein : abbreviated protein name
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1590 # - Gene : HUGO gene name
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1591 # - Peptide : peptide sequence without indications of phosphorylation
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1592 # - Reside.Both : position(s) of phosphorylation within Gene sequence
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1593 # - First letter designates AA that is modified
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1594 # - Numbers indicate position within Gene
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1595 # - Multiple values are separated by semicolons
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1596 # - p : p-value
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1597 # - FC : fold-change
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diff changeset
1598 px,
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diff changeset
1599
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1600 # A binary input of TRUE or FALSE, indicating whether or not to include
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1601 # NetworKIN predictions
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diff changeset
1602 networkin,
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diff changeset
1603
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diff changeset
1604 # A numeric value between 1 and infinity setting the minimum NetworKIN
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1605 # score (can be left out if networkin = FALSE)
26
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diff changeset
1606 networkin_cutoff,
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diff changeset
1607
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diff changeset
1608 # Minimum substrate count, necessary to adjust the p-value appropriately.
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diff changeset
1609 minimum_substrate_count
22
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diff changeset
1610
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1611 ) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1612 # no px$FC should be <= 0, but abs(px$FC) is used below as a precaution.
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1613 if (length(grep(";", px$Residue.Both)) == 0) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1614 # There are no Residue.Both entries having semicolons, so new is
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1615 # simply px except two columns are renamed and a column is added
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1616 # for log2(abs(fold-change))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1617 new <- px
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1618 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1619 new$log2_fc <- log2(abs(as.numeric(as.character(new$FC))))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1620 new <- new[complete.cases(new$log2_fc), ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1621 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1622 # Split each row having semicolons in Residue.Both into rows that are
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1623 # duplicated in all respects except that each row has a single
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1624 # member of the set "split-on-semicolon-Residue.Both"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1625 px_double <- px[grep(";", px$Residue.Both), ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1626 residues <- as.character(px_double$Residue.Both)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1627 residues <- as.matrix(residues, ncol = 1)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1628 split <- strsplit(residues, split = ";")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1629 # x gets count of residues in each row,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1630 # i.e., 1 + count of semicolons
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1631 x <- sapply(split, length)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1632 # Here is the set of split rows
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1633 px_single <- data.frame(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1634 Protein = rep(px_double$Protein, x),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1635 Gene = rep(px_double$Gene, x),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1636 Peptide = rep(px_double$Peptide, x),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1637 Residue.Both = unlist(split),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1638 p = rep(px_double$p, x),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1639 FC = rep(px_double$FC, x)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1640 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1641 # new first gets the split rows
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1642 new <- px[-grep(";", px$Residue.Both), ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1643 # to new, append the rows that didn't need splitting in the first place
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1644 new <- rbind(new, px_single)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1645 # map Gene to SUB_GENE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1646 # map Residue.Both to SUB_MOD_RSD
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1647 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1648 # Eliminate any non-positive values to prevent introduction of
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1649 # infinite or NaN values
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1650 new[(0 <= new$log2_fc), "log2_fc"] <- NA
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1651 # Because of preceding step, there is no need for abs in the next line
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1652 new$log2_fc <- log2(as.numeric(as.character(new$FC)))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1653 # Convert any illegal values from NaN to NA
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1654 new[is.nan(new$log2_fc), "log2_fc"] <- NA
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1655 # Eliminate rows having missing values (e.g., non-imputed data)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1656 new <- new[complete.cases(new$log2_fc), ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1657 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1658 # At this point, new$log2_fc is signed according to which contrast has
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1659 # the greater intensity
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1660 # To take the magnitude into account without taking the direction into
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1661 # account, set params$kseaUseAbsoluteLog2FC to TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1662 #
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1663 # Should KSEA be performed aggregating signed log2FC or absolute?
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1664 # FALSE use raw log2FC for KSEA as for KSEAapp::KSEA.Scores
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1665 if (params$kseaUseAbsoluteLog2FC) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1666 # TRUE use abs(log2FC) for KSEA as Justin requested; this is a
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1667 # justifiable deviation from the KSEAapp::KSEA.Scores algorithm.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1668 new$log2_fc <- abs(new$log2_fc)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1669 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
1670
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1671 monitor_filtration_on_stderr <- TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1672 if (monitor_filtration_on_stderr) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1673 # set to TRUE to monitor filtration on stderr
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1674 sink(stderr())
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1675 cat(see_variable(networkin, "\n"))
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1676 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1677 ksdata_filtered <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1678 sqldf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1679 sprintf("%s %s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1680 "select * from ksdata where not Source = 'NetworKIN'",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1681 if (networkin)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1682 sprintf("or networkin_score >= %d", networkin_cutoff)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1683 else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1684 ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1685 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1686 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1687 if (monitor_filtration_on_stderr) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1688 cat(see_variable(sqldf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1689 "select count(*), Source from ksdata group by Source"), "\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1690 cat(see_variable(sqldf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1691 "select count(*), Source from ksdata_filtered group by Source"), "\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1692 sink()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1693 }
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diff changeset
1694
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diff changeset
1695 ############################################################################
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diff changeset
1696 # Line numbers below refer to lines of:
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diff changeset
1697 # https://github.com/casecpb/KSEAapp/blob/master/R/KSEA.Scores.R
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diff changeset
1698 # I would put the original line in a comment but then lint would complain...
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diff changeset
1699 # - Indeed, I had to rename all the variables because lint didn't like names
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diff changeset
1700 # containing periods or capital letters.
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diff changeset
1701 # ACE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1702 ############################################################################
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diff changeset
1703 #
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diff changeset
1704 # (1) Join the two data.frames on common columns SUB_GENE and SUB_MOD_RSD
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1705 # colnames of ksdata_filtered:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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1706 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE" "SUB_GENE_ID"
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diff changeset
1707 # "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD" "SITE_GRP_ID"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1708 # "SITE_...7_AA" "networkin_score" "Source"
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diff changeset
1709 # colnames of new:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1710 # "Protein" "SUB_GENE" "Peptide" "SUB_MOD_RSD" "p" "FC" "log2_fc"
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diff changeset
1711 # Equivalent to:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1712 # SELECT a.*. b.Protein, b.Peptide, b.p, b.FC, b.log2_fc
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diff changeset
1713 # FROM ksdata_filtered a
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1714 # INNER JOIN new b
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1715 # ON a.SUB_GENE = b.SUB_GENE
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1716 # AND a.SUB_MOD_RSD = b.SUB_MOD_RSD
26
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diff changeset
1717 # (KSEA.Scores.R line # 105)
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diff changeset
1718 # "Extract KSData.filtered annotations that are only found in new"
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1719 ksdata_dataset <- base::merge(ksdata_filtered, new)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1720 # colnames of ksdata_dataset:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1721 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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1722 # "SUB_GENE_ID" "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD"
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diff changeset
1723 # "SITE_GRP_ID" "SITE_...7_AA" "networkin_score" "Source" "Protein"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1724 # "Peptide" "p" "FC" "log2_fc" (uniprot_no_isoform)
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1725 # Re-order dataset; prior to accounting for isoforms
26
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diff changeset
1726 # (KSEA.Scores.R line # 106)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1727 ksdata_dataset <- ksdata_dataset[order(ksdata_dataset$GENE), ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1728 # Extract non-isoform accession in UniProtKB
26
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diff changeset
1729 # (KSEA.Scores.R line # 107)
22
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diff changeset
1730 ksdata_dataset$uniprot_no_isoform <- sapply(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1731 ksdata_dataset$KIN_ACC_ID,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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1732 function(x) unlist(strsplit(as.character(x), split = "-"))[1]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1733 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1734 # "last expression collapses isoforms ... for easy processing"
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1735 # Discard previous results while selecting interesting columns ...
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1736 # (KSEA.Scores.R line # 110)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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1737 ksdata_dataset_abbrev <- ksdata_dataset[, c(5, 1, 2, 16:19, 14)]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1738 # Column names are now:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1739 # "GENE" "SUB_GENE" "SUB_MOD_RSD" "Peptide" "p"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1740 # "FC" "log2_fc" "Source"
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diff changeset
1741 # Make column names human-readable
26
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diff changeset
1742 # (KSEA.Scores.R line # 111)
22
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1743 colnames(ksdata_dataset_abbrev) <- c(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1744 "Kinase.Gene", "Substrate.Gene", "Substrate.Mod", "Peptide", "p",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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1745 "FC", "log2FC", "Source"
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diff changeset
1746 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1747 # SELECT * FROM ksdata_dataset_abbrev
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1748 # ORDER BY Kinase.Gene, Substrate.Gene, Substrate.Mod, p
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1749 # (KSEA.Scores.R line # 112)
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diff changeset
1750 # "Extract KSData.filtered annotations that are only found in new"
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1751 ksdata_dataset_abbrev <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1752 ksdata_dataset_abbrev[
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1753 order(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1754 ksdata_dataset_abbrev$Kinase.Gene,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1755 ksdata_dataset_abbrev$Substrate.Gene,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1756 ksdata_dataset_abbrev$Substrate.Mod,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1757 ksdata_dataset_abbrev$p),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1758 ]
26
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1759 if (print_nb_messages) nbe(see_variable(ksdata_dataset_abbrev))
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1760 # First aggregation step to account for multiply phosphorylated peptides
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1761 # and differing peptide sequences; the goal here is to combine results
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diff changeset
1762 # for all measurements of the same substrate.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1763 # SELECT `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1764 # `Source`, avg(log2FC) AS log2FC
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diff changeset
1765 # FROM ksdata_dataset_abbrev
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1766 # GROUP BY `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1767 # `Source`
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1768 # ORDER BY `Kinase.Gene`;
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diff changeset
1769 # in two steps:
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diff changeset
1770 # (1) compute average log_2(fold-change)
26
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diff changeset
1771 # "take the mean of the log2FC amongst phosphosite duplicates"
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diff changeset
1772 # (KSEA.Scores.R line # 115)
22
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diff changeset
1773 ksdata_dataset_abbrev <- aggregate(
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1774 log2FC ~ Kinase.Gene + Substrate.Gene + Substrate.Mod + Source,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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1775 data = ksdata_dataset_abbrev,
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diff changeset
1776 FUN = mean
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1777 )
26
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diff changeset
1778 if (print_nb_messages) nbe(see_variable(ksdata_dataset_abbrev))
22
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diff changeset
1779 # (2) order by Kinase.Gene
26
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diff changeset
1780 # (KSEA.Scores.R line # 117)
22
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diff changeset
1781 ksdata_dataset_abbrev <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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1782 ksdata_dataset_abbrev[order(ksdata_dataset_abbrev$Kinase.Gene), ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1783 # SELECT `Kinase.Gene`, count(*)
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diff changeset
1784 # FROM ksdata_dataset_abbrev
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1785 # GROUP BY `Kinase.Gene`;
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diff changeset
1786 # in two steps:
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diff changeset
1787 # (1) Extract the list of Kinase.Gene names
26
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1788 # "@@@@@@@@@@@@@@@@@@@@"
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diff changeset
1789 # "Do analysis for KSEA"
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diff changeset
1790 # "@@@@@@@@@@@@@@@@@@@@"
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diff changeset
1791 # (KSEA.Scores.R line # 124)
22
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diff changeset
1792 kinase_list <- as.vector(ksdata_dataset_abbrev$Kinase.Gene)
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diff changeset
1793 # (2) Convert to a named list of counts of kinases in ksdata_dataset_abrev,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1794 # named by Kinase.Gene
26
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diff changeset
1795 # (KSEA.Scores.R line # 125)
22
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diff changeset
1796 kinase_list <- as.matrix(table(kinase_list))
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diff changeset
1797 # Second aggregation step to account for all substrates per kinase
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diff changeset
1798 # CREATE TABLE mean_fc
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diff changeset
1799 # AS
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diff changeset
1800 # SELECT `Kinase.Gene`, avg(log2FC) AS log2FC
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diff changeset
1801 # FROM ksdata_dataset_abbrev
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1802 # GROUP BY `Kinase.Gene`
26
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diff changeset
1803 # (KSEA.Scores.R line # 127)
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diff changeset
1804 if (print_nb_messages) nb(see_variable(ksdata_dataset_abbrev), "\n")
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diff changeset
1805 mean_fc <-
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diff changeset
1806 aggregate(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1807 log2FC ~ Kinase.Gene,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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1808 data = ksdata_dataset_abbrev,
26
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diff changeset
1809 FUN = mean
22
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diff changeset
1810 )
26
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diff changeset
1811 if (print_nb_messages) nbe(see_variable(mean_fc), "\n")
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diff changeset
1812
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diff changeset
1813 # for contrast j
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diff changeset
1814 # for each kinase i
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diff changeset
1815 # extract log2 of fold-change (from `new` above)
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diff changeset
1816 # (used in KSEA.Scores.R lines # 130 & 132)
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diff changeset
1817 log2_fc_j_each_i <-
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diff changeset
1818 new$log2_fc
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diff changeset
1819
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diff changeset
1820 # for contrast j
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diff changeset
1821 # for all kinases i
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diff changeset
1822 # compute mean of abs(log2 of fold-change)
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diff changeset
1823 # (used in KSEA.Scores.R lines # 130)
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diff changeset
1824 mean_abs_log2_fc_j_all_i <-
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1825 mean(abs(log2_fc_j_each_i), na.rm = TRUE)
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diff changeset
1826
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1827 # for contrast j
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diff changeset
1828 # for all kinases i
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diff changeset
1829 # compute mean of log2 of fold-change
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diff changeset
1830 # (used in KSEA.Scores.R lines # 132)
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diff changeset
1831 mean_log2_fc_j_all_i <-
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diff changeset
1832 mean(log2_fc_j_each_i, na.rm = TRUE)
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diff changeset
1833
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1834 # Reorder mean_fc, although I don't see why
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1835 # (KSEA.Scores.R line 128
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1836 mean_fc <- mean_fc[order(mean_fc[, 1]), ]
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1837 # mean_fc columns so far: "Kinase.Gene", "log2FC"
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1838 # - Kinase.Gene
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1839 # indicates the gene name for each kinase.
22
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1840
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1841 # Create column 3: mS
26
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1842 # - mS
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1843 # represents the mean log2(fold change) of all the
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1844 # kinase's substrates.
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1845 # (KSEA.Scores.R line # 129)
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1846 mean_fc$m_s <-
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1847 mean_fc_m_s <- mean_fc[, 2]
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1848
22
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1849 # Create column 4: Enrichment
26
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1850 # - Enrichment
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1851 # is the background-adjusted value of the kinase's mS.
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1852 # (KSEA.Scores.R line # 130)
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1853 mean_fc$enrichment <-
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1854 mean_fc_m_s / mean_abs_log2_fc_j_all_i
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diff changeset
1855
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diff changeset
1856 # Create column 5: m, count of substrates of kinase (count of j for i)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1857 # - m
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diff changeset
1858 # is the total number of detected substrates
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1859 # from the experimental dataset for each kinase.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1860 # (KSEA.Scores.R line # 131)
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diff changeset
1861 mean_fc$m <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1862 mean_fc_m <- kinase_list
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1863
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diff changeset
1864
22
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diff changeset
1865 # Create column 6: z-score
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1866 # - z.score
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1867 # is the normalized score for each kinase, weighted by
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1868 # the number of identified substrates.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1869 # (KSEA.Scores.R line # 132)
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diff changeset
1870 mean_fc$z_score <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1871 (mean_fc_m_s - mean_log2_fc_j_all_i) * sqrt(mean_fc_m) /
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1872 sd(log2_fc_j_each_i, na.rm = TRUE)
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diff changeset
1873
22
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diff changeset
1874 # Create column 7: p-value, deduced from z-score
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1875 # - p.value
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diff changeset
1876 # represents the statistical assessment for the z.score.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1877 # (KSEA.Scores.R line # 133)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1878 # "one-tailed p-value"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1879 mean_fc$p_value <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1880 pnorm(-abs(mean_fc$z_score))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1881
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1882 # zap excluded kinases; this must be done before adjusting p-value
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1883 if (TRUE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1884 mean_fc <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1885 mean_fc[
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1886 mean_fc$m >= minimum_substrate_count,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1887 ,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1888 drop = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1889 ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1890 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1891
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1892 #ACE nb(see_variable(nrow(mean_fc)), "\n")
22
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diff changeset
1893 # Create column 8: FDR, deduced by Benjamini-Hochberg adustment from p-value
26
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diff changeset
1894 # - FDR
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1895 # is the p-value adjusted for multiple hypothesis testing
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1896 # using the Benjamini & Hochberg method."
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1897 # (KSEA.Scores.R line # 134)
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diff changeset
1898 mean_fc$fdr <-
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diff changeset
1899 p.adjust(mean_fc$p_value, method = "fdr")
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diff changeset
1900
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diff changeset
1901 # It makes no sense to leave Z-scores negative when using
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1902 # absolute value of fold-change
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diff changeset
1903 if (params$kseaUseAbsoluteLog2FC) {
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diff changeset
1904 mean_fc$z_score <- abs(mean_fc$z_score)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1905 }
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diff changeset
1906
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diff changeset
1907 # Remove second column (log2FC), which is duplicated as mS
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1908 # (KSEA.Scores.R line # 136)
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diff changeset
1909 mean_fc <-
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diff changeset
1910 mean_fc[order(mean_fc$Kinase.Gene), -2]
22
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diff changeset
1911 # Correct the column names which we had to hack because of the linter...
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diff changeset
1912 colnames(mean_fc) <- c(
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diff changeset
1913 "Kinase.Gene", "mS", "Enrichment", "m", "z.score", "p.value", "FDR"
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diff changeset
1914 )
26
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diff changeset
1915 # (KSEA.Scores.R line # 138)
22
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diff changeset
1916 return(mean_fc)
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diff changeset
1917 }
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diff changeset
1918
26
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diff changeset
1919 ksea_low_fdr_barplot_factory <- function(
22
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diff changeset
1920 rslt,
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diff changeset
1921 i_cntrst,
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diff changeset
1922 i,
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diff changeset
1923 a_level,
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diff changeset
1924 b_level,
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diff changeset
1925 fold_change,
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diff changeset
1926 caption
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diff changeset
1927 ) {
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1928 rslt_score_list_i <- rslt$score_list[[i]]
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1929 if (!is.null(rslt_score_list_i)) {
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diff changeset
1930 rslt_score_list_i_nrow <- nrow(rslt_score_list_i)
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diff changeset
1931 k <- data.frame(
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diff changeset
1932 contrast = as.integer(i_cntrst),
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diff changeset
1933 a_level = rep.int(a_level, rslt_score_list_i_nrow),
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diff changeset
1934 b_level = rep.int(b_level, rslt_score_list_i_nrow),
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diff changeset
1935 kinase_gene = rslt_score_list_i$Kinase.Gene,
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diff changeset
1936 mean_log2_fc = rslt_score_list_i$mS,
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1937 enrichment = rslt_score_list_i$Enrichment,
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diff changeset
1938 substrate_count = rslt_score_list_i$m,
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diff changeset
1939 z_score = rslt_score_list_i$z.score,
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diff changeset
1940 p_value = rslt_score_list_i$p.value,
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1941 fdr = rslt_score_list_i$FDR
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diff changeset
1942 )
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diff changeset
1943 selector <- switch(
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1944 ksea_cutoff_statistic,
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1945 "FDR" = {
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diff changeset
1946 k$fdr
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diff changeset
1947 },
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diff changeset
1948 "p.value" = {
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1949 k$p_value
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1950 },
26
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diff changeset
1951 {
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diff changeset
1952 cat(
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diff changeset
1953 sprintf(
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diff changeset
1954 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'",
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1955 ksea_cutoff_statistic
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diff changeset
1956 )
22
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diff changeset
1957 )
26
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1958 param_df_exit()
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1959 knitr::knit_exit()
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1960 }
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diff changeset
1961 )
22
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1962
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1963 k <- k[selector < ksea_cutoff_threshold, ]
26
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1964 nrow_k <- nrow(k)
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1965
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diff changeset
1966 #ACE nbe(see_variable(fdr_barplot_dataframe <- k))
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1967
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1968 if (nrow_k > 0) {
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1969 max_nchar_rowname <- max(nchar(rownames(k)))
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1970 my_cex_names <- 1.0 / (1 + nrow_k / 50)
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diff changeset
1971
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diff changeset
1972 if (print_trace_messages) cat_margins("Initially")
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diff changeset
1973 if (print_trace_messages) cat_variable(nrow_k, "\n\n", 0)
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diff changeset
1974 if (print_trace_messages) cat_variable(my_cex_names, "\n\n", 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
1975 if (print_trace_messages) cat_variable(max_nchar_rowname, "\n\n", 0)
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diff changeset
1976
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diff changeset
1977 # fin: The figure region dimensions, (width, height), in inches.
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diff changeset
1978 # mar: A numerical vector of the form c(bottom, left, top, right)
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diff changeset
1979 # that gives the number of lines of margin to be specified
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diff changeset
1980 # on the four sides of the plot; default: c(5, 4, 4, 2) + 0.1
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diff changeset
1981
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diff changeset
1982 # mar: The figure region dimensions, (width, height), in inches.
22
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diff changeset
1983 numeric_z_score <- as.numeric(k$z_score)
26
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1984 bar_order <- order(-as.numeric(k$p_value))
22
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diff changeset
1985 kinase_name <- k$kinase_gene
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diff changeset
1986 long_caption <-
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diff changeset
1987 sprintf(
26
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diff changeset
1988 "Kinase z-score, %s, KSEA %s < %s",
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diff changeset
1989 caption,
22
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diff changeset
1990 ksea_cutoff_statistic,
26
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diff changeset
1991 ksea_cutoff_threshold
22
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diff changeset
1992 )
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diff changeset
1993 my_cex_caption <- 65.0 / max(65.0, nchar(long_caption))
26
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diff changeset
1994 # return a function that draws the plot
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diff changeset
1995 function() {
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diff changeset
1996 par_fin <- par("fin") # vector of width_in_inches and height_in_inches)
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diff changeset
1997 op <- par(
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diff changeset
1998 bg = if (print_trace_messages) "yellow" else "white",
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diff changeset
1999 fin = c(par_fin[1], min(par_fin[2], 2.5 + nrow_k / 6)),
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diff changeset
2000 mar = par("mar") +
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diff changeset
2001 c(3 / nrow_k, (1 + max_nchar_rowname * my_cex_names) / 2, 0, 0)
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diff changeset
2002 # bottom, left, top, right
24
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diff changeset
2003 )
26
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diff changeset
2004 on.exit(par(op))
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diff changeset
2005 if (print_trace_messages) cat_margins("Eventually")
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diff changeset
2006
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diff changeset
2007 barplot(
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diff changeset
2008 height = numeric_z_score[bar_order],
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diff changeset
2009 border = NA,
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diff changeset
2010 xpd = FALSE,
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diff changeset
2011 cex.names = my_cex_names,
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diff changeset
2012 main = long_caption,
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diff changeset
2013 cex.main = my_cex_caption,
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diff changeset
2014 names.arg = kinase_name[bar_order],
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diff changeset
2015 horiz = TRUE,
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diff changeset
2016 srt = 45,
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diff changeset
2017 las = 1,
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diff changeset
2018 cex.axis = 0.9
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diff changeset
2019 )
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diff changeset
2020 }
22
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parents: 15
diff changeset
2021 }
26
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diff changeset
2022 } else {
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diff changeset
2023 no_op
22
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diff changeset
2024 }
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diff changeset
2025 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2026
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2027 # note that this adds elements to the global variable `ksea_asterisk_hash`
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2028
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2029 ksea_low_fdr_print <- function(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2030 rslt,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2031 i_cntrst,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2032 i,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2033 a_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2034 b_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2035 fold_change,
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2036 caption,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2037 write_db = TRUE, # if TRUE, write to DB, else print table
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2038 anchor = c(const_table_anchor_p, const_table_anchor_t)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2039 ) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2040 rslt_score_list_i <- rslt$score_list[[i]]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2041 if (!is.null(rslt_score_list_i)) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2042 rslt_score_list_i_nrow <- nrow(rslt_score_list_i)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2043 k <- contrast_ksea_scores <- data.frame(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2044 contrast = as.integer(i_cntrst),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2045 a_level = rep.int(a_level, rslt_score_list_i_nrow),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2046 b_level = rep.int(b_level, rslt_score_list_i_nrow),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2047 kinase_gene = rslt_score_list_i$Kinase.Gene,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2048 mean_log2_fc = rslt_score_list_i$mS,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2049 enrichment = rslt_score_list_i$Enrichment,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2050 substrate_count = rslt_score_list_i$m,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2051 z_score = rslt_score_list_i$z.score,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2052 p_value = rslt_score_list_i$p.value,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2053 fdr = rslt_score_list_i$FDR
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2054 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2055
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2056 selector <- switch(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2057 ksea_cutoff_statistic,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
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diff changeset
2058 "FDR" = {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2059 k$fdr
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2060 },
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2061 "p.value" = {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2062 k$p_value
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2063 },
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2064 {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2065 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2066 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2067 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2068 ksea_cutoff_statistic
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2069 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2070 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2071 param_df_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2072 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2073 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2074 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2075
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2076 k <- k[selector < ksea_cutoff_threshold, ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2077 # save kinase names to ksea_asterisk_hash
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2078 for (kinase_name in k$kinase_gene) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2079 ksea_asterisk_hash[[kinase_name]] <- 1
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2080 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2081
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2082 if (write_db) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2083 db_write_table_overwrite <- (i_cntrst < 2)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2084 db_write_table_append <- !db_write_table_overwrite
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2085 RSQLite::dbWriteTable(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2086 conn = db,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2087 name = "contrast_ksea_scores",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2088 value = contrast_ksea_scores,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2089 append = db_write_table_append
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2090 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2091 ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2092 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2093 selector <- switch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2094 ksea_cutoff_statistic,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2095 "FDR" = {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2096 contrast_ksea_scores$fdr
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2097 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2098 "p.value" = {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2099 contrast_ksea_scores$p_value
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2100 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2101 {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2102 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2103 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2104 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2105 ksea_cutoff_statistic
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2106 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2107 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2108 param_df_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2109 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2110 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2111 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2112 if (print_nb_messages) nbe(see_variable(contrast_ksea_scores))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2113 output_df <- contrast_ksea_scores[
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2114 selector < ksea_cutoff_threshold,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2115 c("kinase_gene", "mean_log2_fc", "enrichment", "substrate_count",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2116 "z_score", "p_value", "fdr")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2117 ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2118 output_df$kinase_gene <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2119 gsub(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2120 "_",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2121 "\\\\_",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2122 output_df$kinase_gene
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2123 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2124 colnames(output_df) <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2125 c(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2126 colnames(output_df)[1],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2127 colnames(output_df)[2],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2128 "enrichment",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2129 "m_s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2130 "z_score",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2131 "p_value",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2132 "fdr"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2133 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2134 #ACE output_order <- with(output_df, order(fdr))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2135 output_order <- with(output_df, order(p_value))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2136 output_df <- output_df[output_order, ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2137
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2138 output_df[, 2] <- sprintf("%0.3g", output_df[, 2])
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2139 output_df$fdr <- sprintf("%0.4f", output_df$fdr)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2140 output_df$p_value <- sprintf("%0.2e", output_df$p_value)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2141 output_df$z_score <- sprintf("%0.2f", output_df$z_score)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2142 output_df$m_s <- sprintf("%d", output_df$m_s)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2143 output_df$enrichment <- sprintf("%0.3g", output_df$enrichment)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2144 output_ncol <- ncol(output_df)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2145 colnames(output_df) <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2146 c(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2147 "Kinase",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2148 "\\(\\overline{{\\lvert}\\log_2 (\\text{fold-change}){\\rvert}}\\)",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2149 "Enrichment",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2150 "Substrates",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2151 "z-score",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2152 "p-value",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2153 "FDR"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2154 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2155 selector <- switch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2156 ksea_cutoff_statistic,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2157 "FDR" = {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2158 rslt$score_list[[i]]$FDR
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2159 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2160 "p.value" = {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2161 rslt$score_list[[i]]$p.value
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2162 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2163 {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2164 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2165 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2166 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2167 ksea_cutoff_statistic
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2168 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2169 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2170 param_df_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2171 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2172 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2173 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2174 if (sum(selector < ksea_cutoff_threshold) > 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2175 if (print_nb_messages) nbe(see_variable(output_df))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2176 math_caption <- gsub("{", "\\{", caption, fixed = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2177 math_caption <- gsub("}", "\\}", math_caption, fixed = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2178 # with (
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2179 # output_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2180 # )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2181 if (TRUE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2182 output_df$Kinase <- whack_underscores(output_df$Kinase)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2183 data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2184 x = output_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2185 # vector of tab stops, in inches
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2186 tabstops = c(1.0, 1.2, 1.0, 1.0, 1.0, 1.0),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2187 # vector of headings, registered with tab-stops
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2188 headings = colnames(output_df),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2189 # digits to pass to format.data.frame
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2190 digits = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2191 # maximumn number of rows to print
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2192 max = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2193 # optional caption
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2194 caption = sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2195 "\\text{%s}, KSEA %s < %s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2196 math_caption,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2197 ksea_cutoff_statistic,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2198 ksea_cutoff_threshold
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2199 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2200 # set underscore_whack to TRUE to escape underscores
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2201 underscore_whack = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2202 # flag for landscape mode
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2203 landscape = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2204 # flag indicating that subsubsection should be used for caption
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2205 # rather than subsection
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2206 use_subsubsection_header = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2207 # character-size indicator; for possible values, see:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2208 # https://tug.org/texinfohtml/latex2e.html#Font-sizes
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2209 charactersize = "small",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2210 # set verbatim to TRUE to debug output
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2211 verbatim = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2212 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2213 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2214 data_frame_table_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2215 x = output_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2216 justification = "l c c c c c c",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2217 centered = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2218 caption = sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2219 "\\text{%s}, KSEA %s < %s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2220 math_caption,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2221 ksea_cutoff_statistic,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2222 ksea_cutoff_threshold
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2223 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2224 anchor = anchor,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2225 underscore_whack = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2226 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2227 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2228 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2229 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2230 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2231 "\\break
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2232 No kinases had
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2233 \\(\\text{KSEA %s}_\\text{enrichment} < %s\\)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2234 for contrast %s\\hfill\\break\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2235 ksea_cutoff_statistic,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2236 ksea_cutoff_threshold,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2237 caption
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2238 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2239 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2240 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2241 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2242 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2243 ""
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2244 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2245 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2246
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2247 # create_breaks is a helper for ksea_heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2248 create_breaks <- function(merged_scores) {
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2249 if (sum(!is.na(merged_scores)) < 2)
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2250 return(NULL)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2251 if (min(merged_scores, na.rm = TRUE) < -1.6) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2252 breaks_neg <- seq(-1.6, 0, length.out = 30)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2253 breaks_neg <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2254 append(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2255 seq(min(merged_scores, na.rm = TRUE), -1.6, length.out = 10),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2256 breaks_neg
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2257 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2258 breaks_neg <- sort(unique(breaks_neg))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2259 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2260 breaks_neg <- seq(-1.6, 0, length.out = 30)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2261 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2262 if (max(merged_scores, na.rm = TRUE) > 1.6) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2263 breaks_pos <- seq(0, 1.6, length.out = 30)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2264 breaks_pos <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2265 append(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2266 breaks_pos,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2267 seq(1.6, max(merged_scores, na.rm = TRUE),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2268 length.out = 10)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2269 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2270 breaks_pos <- sort(unique(breaks_pos))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2271 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2272 breaks_pos <- seq(0, 1.6, length.out = 30)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2273 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2274 breaks_all <- unique(append(breaks_neg, breaks_pos))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2275 mycol_neg <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2276 gplots::colorpanel(n = length(breaks_neg),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2277 low = "blue",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2278 high = "white")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2279 mycol_pos <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2280 gplots::colorpanel(n = length(breaks_pos) - 1,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2281 low = "white",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2282 high = "red")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2283 mycol <- unique(append(mycol_neg, mycol_pos))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2284 color_breaks <- list(breaks_all, mycol)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2285 return(color_breaks)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2286 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2287
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2288 hm2plus <- function(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2289 x,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2290 mat = matrix(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2291 c(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2292 c(0, 4, 0),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2293 c(0, 3, 3),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2294 c(2, 1, 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2295 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2296 nrow = 3,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2297 ncol = 3,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2298 byrow = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2299 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2300 denwid = 0.5,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2301 denhgt = 0.15,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2302 widths = c(0.5, 2.5, 1.5),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2303 heights = c(0.4, 0.15, 3.95),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2304 divergent = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2305 notecol = "grey50",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2306 trace = "none",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2307 margins = c(6, 20),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2308 srtcol = 90,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2309 srtrow = 0,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2310 density_info = "none",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2311 key_xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2312 key_par = list(),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2313 hclustfun = hclust,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2314 ...
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2315 ) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2316
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2317 varargs <- list(...)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2318 if (FALSE) # this is to avoid commenting out code to pass linting...
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2319 my_hm2 <- latex_show_invocation(heatmap.2, head_patch = FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2320 else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2321 my_hm2 <- heatmap.2
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2322
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2323 x <- as.matrix(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2324 if (sum(!is.na(x)) < 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2325 return(NULL)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2326 color_count <- 1 + max(64, length(as.vector(x))) # 8 was not enough
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2327 break_count <- 1 + color_count
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2328 min_nonax <- min(x, na.rm = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2329 max_nonax <- max(x, na.rm = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2330 if (print_nb_messages) nb("within hm2plus", see_variable(divergent), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2331 if (divergent) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2332 zlim <- max(abs(min_nonax), abs(max_nonax))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2333 if (print_nb_messages) nb(see_variable(pre_zlim <- zlim, "\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2334 breaks <- (zlim) / (break_count:1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2335 if (print_nb_messages) nb(see_variable(breaks, "\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2336 breaks <- breaks - median(breaks)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2337 zlim <- c(-zlim, zlim)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2338 if (print_nb_messages) nb(see_variable(zlim, "\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2339 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2340 zlim <- max(abs(min_nonax), abs(max_nonax))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2341 if (print_nb_messages) nb(see_variable(pre_zlim <- zlim, "\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2342 breaks <- zlim / (break_count:1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2343 if (print_nb_messages) nb(see_variable(breaks, "\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2344 if (max_nonax < 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2345 breaks <- breaks - zlim
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2346 zlim <- c(-zlim, 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2347 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2348 zlim <- c(0, zlim)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2349 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2350 if (print_nb_messages) nb(see_variable(zlim, "\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2351 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2352 nonax <- x
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2353 nonax[is.na(x)] <- min_nonax
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2354 if (is.null(widths)) widths <- c(denwid, 4 - denwid, 1.5)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2355 if (is.null(heights)) heights <- c(0.4, denhgt, 4.0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2356 colors <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2357 if (divergent && min_nonax < 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2358 # divergent colors on both sides of zero
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2359 colorRampPalette(c("red", "white", "blue"))(color_count)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2360 } else if (divergent && min_nonax > 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2361 # "divergent" colors > zero
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2362 colorRampPalette(c("white", "blue"))(color_count)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2363 } else if (divergent && max_nonax < 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2364 # "divergent" colors < zero
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2365 colorRampPalette(c("red", "white"))(color_count)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2366 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2367 # "non-divergent" colors including zero
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2368 hcl.colors(color_count, "YlOrRd", rev = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2369 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2370
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2371 #ACE if (print_nb_messages) nb("within hm2plus", see_variable(key_par), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2372 #ACE if (print_nb_messages) nb(see_variable(colors, "\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2373 #ACE key_par$col = colors
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2374 #ACE key_par$breaks = breaks
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2375
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2376 if (print_nb_messages) nb(see_variable(par(), "\n")) #ACE TODO remove me
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2377 if (print_nb_messages) cat("\\leavevmode\n\\linebreak\n") #ACE TODO remove me
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2378 suppressWarnings(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2379 my_hm2(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2380 x = x,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2381 col = colors,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2382 #ACE symkey = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2383 density.info = density_info,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2384 srtCol = srtcol,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2385 srtRow = srtrow,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2386 margins = margins,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2387 lwid = widths,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2388 lhei = heights,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2389 key.title = NA,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2390 key.xlab = key_xlab,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2391 key.par = key_par,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2392 lmat = mat,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2393 notecol = notecol,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2394 trace = trace,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2395 bg = "yellow",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2396 hclustfun = hclustfun,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2397 #ACE breaks = breaks,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2398 oldstyle = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2399 ... # varargs
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2400 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2401 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2402 # implicitly returning value returned by heatmap.2
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2403 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2404
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2405 # draw_kseaapp_summary_heatmap is a helper function for ksea_heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2406 draw_kseaapp_summary_heatmap <- function(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2407 x, # matrix with row/col names already formatted
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2408 sample_cluster, # a binary input of TRUE or FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2409 # indicating whether or not to perform
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2410 # hierarchical clustering of the sample columns
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2411 merged_asterisk, # matrix having dimensions of x, values "*" or ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2412 color_breaks, # breaks for color gradation, from create_breaks
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2413 # passed to `breaks` argument of `image`
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2414 margins = c(8, 15), # two integers setting the bottom and right margins
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2415 # to accommodate row and column labels
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2416 master_cex = 0.7, # basis for text sizes
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2417 ...
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2418 ) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2419 merged_scores <- x
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2420 if (!is.matrix(x)) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2421 cat(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2422 paste0(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2423 "No plot because \\texttt{typeof(x)} is '",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2424 typeof(x),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2425 "' rather than 'matrix'.\n\n"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2426 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2427 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2428 cat_variable(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2429 return(FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2430 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2431 if (print_trace_messages) cat(sprintf("master_cex = %03f\n\n", master_cex))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2432 nrow_x <- nrow(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2433 ncol_x <- ncol(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2434 #if (nrow_x < 2) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2435 if (nrow_x < 1) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2436 cat("No plot because matrix has no rows.\n\n")
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2437 return(FALSE)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2438 } else if (nrow_x < 2) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2439 cat("No plot because matrix has one row. Matrix looks like this:\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2440 cat("\n\\begin{verbatim}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2441 print(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2442 cat("\n\\end{verbatim}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2443 return(FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2444 } else if (ncol_x < 2) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2445 cat("No plot because matrix x has ", ncol_x, " columns.\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2446 cat_variable(x)
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2447 return(FALSE)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2448 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2449 max_nchar_rowname <- max(nchar(rownames(x)))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2450 max_nchar_colname <- max(nchar(colnames(x)))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2451 my_limit <- g_intensity_hm_rows
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2452
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2453 my_row_cex_scale <- master_cex * 150 / nrow_x
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2454 my_col_cex_scale <- 3.0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2455 my_asterisk_scale <- 0.4 * my_row_cex_scale
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2456 my_row_warp <- 1
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2457 my_note_warp <- 2
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2458 my_row_warp <- 1
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2459 my_row_cex_asterisk <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2460 master_cex * my_row_warp * my_asterisk_scale
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2461
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2462
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2463 my_col_cex <- my_col_cex_scale * master_cex
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2464 my_row_cex <- min(3.5 * my_row_cex_asterisk, my_col_cex)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2465 my_key_cex <- 1.286
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2466 my_hm2_cex <- 1 * master_cex
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2467 my_offset <- (4.8 / (9 + nrow_x / 10)) - 0.4
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2468 if (print_trace_messages) cat(sprintf("nrow_x = %03f\n\n", nrow_x))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2469 if (print_trace_messages) cat(sprintf("my_offset = %03f\n\n", my_offset))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2470 my_offset <- 0.05
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2471 if (print_trace_messages) cat(sprintf("my_offset = %03f\n\n", my_offset))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2472 my_scale <- 3.0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2473 if (ncol_x < 10 && nrow_x < 10)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2474 my_scale <- my_scale * 10 / (10 - nrow_x) * 10 / (10 - ncol_x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2475
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2476 my_heights <- c(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2477 0.15,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2478 3.85 - my_offset,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2479 0.5 + my_offset
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2480 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2481 my_margins <- c(1, 1) +
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2482 c(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2483 margins[1] * 0.08 * max_nchar_colname * my_col_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2484 margins[2] * 0.04 * max_nchar_rowname * my_row_cex
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2485 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2486
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2487 my_notecex <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2488 my_scale *
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2489 min(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2490 1.1,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2491 my_row_cex_asterisk * my_note_warp,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2492 my_col_cex * my_note_warp
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2493 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2494
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2495 if (print_trace_messages) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2496 cat_variable(my_heights, suffix = "; ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2497 cat_variable(my_margins, suffix = "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2498 cat_variable(my_row_cex_scale, suffix = "; ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2499 cat_variable(my_col_cex_scale, suffix = "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2500 cat_variable(my_row_cex_asterisk, suffix = "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2501 cat_variable(my_row_cex, suffix = "; ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2502 cat_variable(my_col_cex, suffix = "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2503 cat_variable(my_row_cex, suffix = "; ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2504 cat_variable(my_col_cex, suffix = "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2505 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2506
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2507 hm2plus(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2508 x = merged_scores,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2509 Colv = sample_cluster,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2510 cellnote = merged_asterisk,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2511 cex = my_hm2_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2512 cexCol = my_col_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2513 cexRow = my_row_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2514 denhgt = 0.15,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2515 density_info = "none",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2516 denwid = 0.5,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2517 divergent = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2518 key_par = list(cex = my_key_cex),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2519 key_xlab = "Z-score",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2520 margins = my_margins,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2521 notecex = my_scale * min(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2522 1.5,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2523 my_row_cex_asterisk * my_note_warp,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2524 my_col_cex * my_note_warp
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2525 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2526 notecol = "white",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2527 scale = "none",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2528 srtcol = 90,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2529 srtrow = 0,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2530 trace = "none",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2531 mat = matrix(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2532 c(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2533 c(0, 3, 3),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2534 c(2, 1, 1),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2535 c(0, 4, 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2536 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2537 nrow = 3,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2538 ncol = 3,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2539 byrow = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2540 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2541 widths = c(0.5, 3.1, 0.9),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2542 heights = my_heights,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2543 ...
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2544 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2545 return(TRUE)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2546 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2547
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2548 # function drawing heatmap of contrast fold-change for each kinase,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2549 # adapted from KSEAapp::KSEA.Heatmap
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2550 ksea_heatmap <- function(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2551 # the data frame outputs from the KSEA.Scores() function, in list format
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2552 score_list,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2553 # a character vector of all the sample names for heatmap annotation:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2554 # - the names must be in the same order as the data in score_list
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2555 # - please avoid long names, as they may get cropped in the final image
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2556 sample_labels,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2557 # character string of either "p.value" or "FDR" indicating the data column
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2558 # to use for marking statistically significant scores
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2559 stats,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2560 # a numeric value between 0 and infinity indicating the min. number of
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2561 # substrates a kinase must have to be included in the heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2562 m_cutoff,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2563 # a numeric value between 0 and 1 indicating the p-value/FDR cutoff
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2564 # for indicating significant kinases in the heatmap
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2565 p_cutoff = {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2566 cat("argument 'p_cutoff' is required for function 'ksea_heatmap'")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2567 param_df_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2568 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2569 },
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2570 # a binary input of TRUE or FALSE, indicating whether or not to perform
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2571 # hierarchical clustering of the sample columns
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2572 sample_cluster,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2573 # a binary input of TRUE or FALSE, indicating whether or not to export
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2574 # the heatmap as a .png image into the working directory
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2575 export = FALSE,
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2576 # bottom and right margins; adjust as needehttps://tex.stackexchange.com/a/56795d if contrast names are too long
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2577 margins = c(6, 6),
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2578 # print which kinases?
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2579 # - Mandatory argument, must be one of const_ksea_.*_kinases
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2580 which_kinases,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2581 # additional arguments to gplots::heatmap.2, such as:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2582 # - main: main title of plot
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2583 # - xlab: x-axis label
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2584 # - ylab: y-axis label
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2585 ...
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2586 ) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2587 filter_m <- function(dataset, m_cutoff) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2588 filtered <- dataset[(dataset$m >= m_cutoff), ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2589 return(filtered)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2590 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2591 score_list_m <- lapply(score_list, function(...) filter_m(..., m_cutoff))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2592 for (i in seq_len(length(score_list_m))) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2593 names <- colnames(score_list_m[[i]])[c(2:7)]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2594 colnames(score_list_m[[i]])[c(2:7)] <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2595 paste(names, i, sep = ".")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2596 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2597 master <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2598 Reduce(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2599 f = function(...) {
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2600 base::merge(..., by = "Kinase.Gene", all = TRUE)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2601 },
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2602 x = score_list_m
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2603 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2604
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2605 row.names(master) <- master$Kinase.Gene
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2606 columns <- as.character(colnames(master))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2607 merged_scores <- as.matrix(master[, grep("z.score", columns), drop = FALSE])
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2608 colnames(merged_scores) <- sample_labels
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2609 merged_stats <- as.matrix(master[, grep(stats, columns)])
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2610 asterisk <- function(mtrx, p_cutoff) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2611 new <- data.frame()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2612 for (i in seq_len(nrow(mtrx))) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2613 for (j in seq_len(ncol(mtrx))) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2614 my_value <- mtrx[i, j]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
2615 if (!is.na(my_value) && my_value < p_cutoff) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2616 new[i, j] <- "*"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2617 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2618 new[i, j] <- ""
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2619 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2620 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2621 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2622 return(new)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2623 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2624 merged_asterisk <- as.matrix(asterisk(merged_stats, p_cutoff))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2625
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2626 asterisk_rows <- rowSums(merged_asterisk == "*") > 0
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2627 all_rows <- rownames(merged_stats)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2628 names(asterisk_rows) <- all_rows
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2629 non_asterisk_rows <- names(asterisk_rows[asterisk_rows == FALSE])
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2630 asterisk_rows <- names(asterisk_rows[asterisk_rows == TRUE])
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2631 merged_scores_asterisk <- merged_scores[names(asterisk_rows), , drop = FALSE]
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2632 merged_scores_non_asterisk <- merged_scores[names(non_asterisk_rows), , drop = FALSE]
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2633
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2634 row_list <- list()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2635 row_list[[const_ksea_astrsk_kinases]] <- asterisk_rows
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2636 row_list[[const_ksea_all_kinases]] <- all_rows
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2637 row_list[[const_ksea_nonastrsk_kinases]] <- non_asterisk_rows
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2638
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2639 i <- which_kinases
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2640 my_row_names <- row_list[[i]]
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2641 scrs <- merged_scores[my_row_names, , drop = FALSE]
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2642 stts <- merged_stats[my_row_names, , drop = FALSE]
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2643 merged_asterisk <- as.matrix(asterisk(stts, p_cutoff))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2644
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2645 color_breaks <- create_breaks(scrs)
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2646 if (is.null(color_breaks)) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2647 cat("No plot because matrix has too few rows.\n\n")
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2648 return(NULL)
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2649 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2650 plot_height <- nrow(scrs) ^ 0.55
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2651 plot_width <- ncol(scrs) ^ 0.7
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2652 if (export == "TRUE") {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2653 png(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2654 "KSEA.Merged.Heatmap.png",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2655 width = plot_width * 300,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2656 height = 2 * plot_height * 300,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2657 res = 300,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2658 pointsize = 14
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2659 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2660 }
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2661 did_draw <- draw_kseaapp_summary_heatmap(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2662 x = scrs,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2663 sample_cluster = sample_cluster,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2664 merged_asterisk = merged_asterisk,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2665 color_breaks = color_breaks,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2666 margins = margins
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2667 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2668 if (export == "TRUE") {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2669 dev.off()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2670 }
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2671 if (!did_draw)
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2672 return(NULL)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2673 return(my_row_names)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2674 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2675
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2676 # helpers for heatmaps of phosphopeptide intensities
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2677
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2678 # factory producing function to truncate string after n characters
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2679 trunc_n <- function(n) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2680 function(x) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2681 sapply(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2682 X = x,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2683 FUN = function(s) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2684 if (is.na(s))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2685 return("NA")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2686 cond <- try_catch_w_e(nchar(s) > n)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2687 if (!is.logical(cond$value)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2688 return(cond$value$message)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2689 } else if (cond$value) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2690 paste0(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2691 strtrim(s, n),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2692 "..."
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2693 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2694 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2695 s
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2696 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2697 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2698 USE.NAMES = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2699 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2700 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2701 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2702 trunc_long_ppep <- function(x) trunc_n(40)(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
2703 trunc_ppep <- function(x) trunc_n(g_ppep_trunc_n)(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
2704 trunc_subgene <- function(x) trunc_n(g_subgene_trunc_n)(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
2705 trunc_enriched_substrate <- function(x) trunc_n(g_sbstr_trunc_n)(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2706
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2707 # factory producing a function that returns a covariance
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2708 # matrix's rows (and columns) having variance > v_min
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2709 keep_cov_w_var_gtr_min <- function(v_min) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2710 function(x) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2711 if (!is.matrix(x))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2712 return(NULL)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2713 keepers <- sapply(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2714 X = seq_len(nrow(x)),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2715 FUN = function(i) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2716 if (x[i, i] < v_min)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2717 NA
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2718 else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2719 x[i, i]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2720 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2721 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2722 names(keepers) <- rownames(x)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2723 keepers <- keepers[!is.na(keepers)]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2724 keepers <- names(keepers)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2725 if (length(keepers) == 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2726 return(NULL)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2727 x[keepers, keepers]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2728 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2729 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2730 # function that returns a matrix's rows having variance > 1
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2731 keep_cov_w_var_gtr_1 <- keep_cov_w_var_gtr_min(1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2732
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2733 # factory producing a function that returns
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2734 # - either a matrix's rows (rows = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2735 # - or a matrix's columns (rows = FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2736 # having variance > v_min
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2737 keep_var_gtr_min <- function(v_min) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2738 function(x, rows = TRUE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2739 nrowcol <- if (rows) nrow else ncol
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2740 if (!is.matrix(x))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2741 return(NULL)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2742 keepers <- sapply(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2743 X = seq_len(nrowcol(x)),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2744 FUN = function(i) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2745 row_var <- var(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2746 if (rows) x[i, ] else x[, i],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2747 na.rm = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2748 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2749 if (is.na(row_var) || row_var <= v_min) NA else i
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2750 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2751 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2752 keepers <- keepers[!is.na(keepers)]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2753 if (rows) x[keepers, ] else x[, keepers]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2754 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2755 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2756
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2757 keep_var_gtr_0 <- keep_var_gtr_min(0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2758
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2759 # function drawing heatmap of phosphopeptide intensities
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2760 ppep_heatmap <-
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2761 function(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2762 m, # matrix with rownames already formatted
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2763 cutoff, # cutoff used by hm_heading_function
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2764 hm_heading_function, # construct $ cat heading from m and cutoff
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2765 hm_main_title, # main title for plot (drawn below heading)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2766 suppress_row_dendrogram = TRUE, # set to false to show dendrogram
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2767 max_peptide_count = # experimental:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2768 g_intensity_hm_rows, # values of 50 and 75 worked well
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2769 master_cex = 1.0, # basis for text sizes
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2770 margins = NULL, # optional margins (bottom, right)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2771 cellnote = NULL, # optional matrix of character; dim = dim(m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2772 adj = 0.5, # adjust text: 0 left, 0.5 middle, 1 right
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
2773 ... # passthru to hm2plus or heatmap.2
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2774 ) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2775 use_heatmap_1 <- FALSE
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2776 peptide_count <- 0
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2777 # emit the heading for the heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2778 if (hm_heading_function(m, cutoff)) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2779 nrow_m <- nrow(m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2780 peptide_count <- min(max_peptide_count, nrow_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2781 if (nrow_m > 1) {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2782 m_margin <- m[peptide_count:1, ]
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2783 # Margin was heuristically derived to accommodate the widest label
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2784 row_mchar_max <- max(nchar(rownames(m_margin)))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2785 col_mchar_max <- max(nchar(colnames(m_margin)))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2786 row_margin <- master_cex * row_mchar_max * 2.6
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2787 col_margin <- master_cex * col_mchar_max * 2.6
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2788 if (print_trace_messages) cat(sprintf("row_margin = %0.3f; ", row_margin))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
2789 if (print_trace_messages) cat(sprintf("col_margin = %0.3f; ", col_margin))
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
2790 hm_call <- NULL
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2791 tryCatch(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2792 {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2793 # set non-argument parameters for hm_call inner function
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2794 my_row_cex <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2795 master_cex * 200000 / (
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2796 (max(nchar(rownames(m_margin)))^2) * g_intensity_hm_rows
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2797 )
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2798 m_hm <- m[peptide_count:1, , drop = FALSE]
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2799 if (is.null(cellnote)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2800 cellnote <- matrix("", nrow = nrow(m_hm), ncol = ncol(m_hm))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2801 cellnote[is.na(m_hm)] <- "NA"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2802 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2803 cellnote <- cellnote[peptide_count:1, , drop = FALSE]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2804 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2805 m_hm[is.na(m_hm)] <- 0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2806 nrow_m_hm <- nrow(m_hm)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2807 ncol_m_hm <- ncol(m_hm)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2808 if (nrow_m_hm < 1 || ncol_m_hm < 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2809 return(peptide_count) # return zero as initialized above
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2810 my_limit <- g_intensity_hm_rows
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2811
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2812
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2813 my_row_cex <- master_cex * (100 / (2 + row_mchar_max))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2814 my_col_cex <- master_cex * 6 * row_margin / col_margin
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2815 my_col_adj <- min(my_col_cex, my_row_cex) / my_col_cex
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2816 my_col_cex <- min(my_col_cex, my_row_cex)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2817 col_margin <- sqrt(my_col_adj) * col_margin
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2818 if (print_trace_messages) cat(sprintf("my_row_cex = %0.3f; ", my_row_cex))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2819 if (print_trace_messages) cat(sprintf("my_col_cex = %0.3f; ", my_col_cex))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2820 if (is.null(margins)) my_margins <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2821 c(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2822 (my_col_cex + col_margin), # col
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2823 (my_row_cex + row_margin) / my_row_cex # row
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2824 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2825 else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2826 my_margins <- margins
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2827
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2828 if (print_trace_messages) cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2829 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2830 "my_margins = c(%s)\n\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2831 paste(my_margins, collapse = ", ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2832 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2833 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2834 my_hm2_cex <- 2 * master_cex
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2835 my_key_cex <- 0.9 - 0.1 * (g_intensity_hm_rows + nrow_m_hm) / g_intensity_hm_rows
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2836 my_key_warp <- 1.5 * 22.75 / row_margin
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2837 my_key_cex <- min(1.10, my_key_warp * my_key_cex)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2838 my_hgt_scale <- 3.70 - 0.4 * (max(1, 0.9 * my_row_cex) - 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2839 my_hgt_scale <- 3.75 # 3.615
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2840 my_hgt_scale <- 3.60 # 3.615
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2841 if (print_trace_messages)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2842 cat_variable(my_hgt_scale, "\n\n", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2843 my_warp <- max(0.1, 1.4 * (7.5 + nrow_m) / g_intensity_hm_rows)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2844 if (print_trace_messages)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2845 cat_variable(my_warp, "\n\n", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2846 # added 0.9 heuristically...
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2847 my_plot_height <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2848 (0.566 + 0.354 * (nrow_m / g_intensity_hm_rows)) *
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2849 min(my_hgt_scale, my_hgt_scale * my_warp)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2850 my_plot_height <- min(3.65, my_plot_height * g_intensity_hm_rows / 50)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2851 my_heights <- c(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2852 0.3, # title and top dendrogram
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2853 my_plot_height, # plot and bottom margin
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2854 4.15 - my_hgt_scale, # legend
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2855 0.05 + my_hgt_scale - my_plot_height # whitespace below legend
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2856 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2857 my_note_cex <- min(0.8, my_row_cex, my_col_cex)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2858 if (print_trace_messages) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2859 cat_variable(my_plot_height, "\n\n", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2860 cat_variable(4.19 - my_hgt_scale, "\n\n", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2861 cat_variable(nrow_m_hm, "; ", 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2862 cat_variable(ncol_m_hm, "; ", 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2863 cat_variable(my_row_cex, "; ", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2864 cat_variable(my_col_cex, "; ", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2865 cat_variable(my_note_cex, "; ", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2866 cat_variable(my_key_cex, "\n\n", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2867 cat_variable(my_hgt_scale, "; ", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2868 cat_variable(my_plot_height, "; ", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2869 cat_variable(my_warp, "\n\n", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2870 cat_variable(my_heights, "; ", 2)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2871 cat_variable(sum(my_heights), "\n\n", 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2872 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2873
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2874 # define hm_call inner function
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2875 hm_call <- function(x, scaling, title) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2876 my_cex_main <- min(5.0, 220 / nchar(title))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2877 op <- par(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2878 cex.main = my_cex_main * master_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2879 adj = adj
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2880 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2881 if (
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2882 !is.null(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2883 hm2plus(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2884 x,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2885 Colv = NA,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2886 Rowv = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2887 cexRow = my_row_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2888 cexCol = my_col_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2889 dendrogram = "row",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2890 las = 1,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2891 main = title,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2892 key_xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2893 cex = my_hm2_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2894 key_par = list(cex = my_key_cex),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2895 margins = my_margins,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2896 widths = c(0.4, 2.6, 1.5),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2897 heights = my_heights,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2898 mat = matrix(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2899 c(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2900 c(0, 3, 3),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2901 c(2, 1, 1),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2902 c(0, 4, 0),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2903 c(0, 0, 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2904 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2905 nrow = 4,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2906 ncol = 3,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2907 byrow = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2908 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2909 na.rm = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2910 scale = scaling,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2911 srtcol = 90,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2912 srtrow = 0,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2913 xlab = "",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2914 cellnote = cellnote,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2915 notecex = my_note_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2916 ...
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2917 )
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2918 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2919 ) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2920 if (print_trace_messages) cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2921 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2922 "my_heights = c(%s); sum = %0.3f\n\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2923 paste(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2924 sprintf("%0.3f", my_heights),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2925 collapse = ", "
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2926 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2927 sum(my_heights)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2928 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2929 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2930 if (print_trace_messages) cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2931 sprintf("my_key_cex = %0.3f\n\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2932 my_key_cex)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2933 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2934 if (print_trace_messages) cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2935 sprintf("my_key_cex/my_heights[3] = %0.3f\n\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2936 my_key_cex / my_heights[3])
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2937 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2938 if (print_trace_messages) cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2939 sprintf("my_heights[2]/my_heights[3] = %0.3f\n\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2940 my_heights[2] / my_heights[3])
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2941 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2942 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2943 par(op)
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2944 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2945
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2946 # invoke hm_call inner function
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2947 if (sum(rowSums(!is.na(m_hm)) < 2))
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2948 hm_call(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2949 m_hm,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2950 "none",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2951 "log(intensities), unscaled, unimputed, and unnormalized"
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2952 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2953 else
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2954 hm_call(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2955 m_hm,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2956 "row",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2957 "log(intensities), row-scaled, unimputed, and unnormalized"
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2958 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2959 },
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2960 error = function(e) {
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2961 if (!is.null(hm_call)) {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2962 m_hm[is.na(m_hm)] <- 0
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2963 tryCatch(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2964 {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2965 if (nrow(m_hm) > 1)
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2966 hm_call(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2967 m_hm,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2968 "none",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2969 paste(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2970 "log(intensities), unscaled,",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2971 "zero-imputed, unnormalized"
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2972 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2973 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2974 else
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2975 cat("\nThere are too few peptides to produce a heatmap.\n")
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2976 },
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2977 error = function(r) {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2978 cat(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2979 sprintf(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2980 "\n%s %s Internal message: %s\n\\newline\n\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2981 "Failure drawing heatmap,",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2982 "possibly because of too many missing values.\n\\newline\n\n",
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2983 r$message
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2984 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2985 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2986 cat_margins()
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2987 }
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2988 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2989 } else {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2990 cat(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2991 "\nFailure drawing heatmap, possibly because of too many missing values.\n"
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2992 )
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2993 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2994 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2995 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2996 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2997 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2998 # return value:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
2999 peptide_count
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3000 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3001
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3002 # function drawing heatmap of correlations if they exist, else covariances
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3003 cov_heatmap <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3004 function(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3005 m, # matrix with rownames already formatted
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3006 top_substrates = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3007 ... # passthru to hm2plus or heatmap.2
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3008 ) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3009 if (print_nb_messages) nbe(see_variable(m), " [", nrow(m), "x", ncol(m), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3010 #ACE nb(rowSums(m, na.rm = TRUE))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3011 #ACE bad_rows <- (rowSums(m, na.rm = TRUE) == 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3012 #ACE nb(see_variable(bad_rows))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3013 #ACE m <- m[-bad_rows, , drop = FALSE]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3014 colnames_m <- colnames(m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3015 is_na_m <- is.na(m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3016 tmp <- m
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3017 tmp[is_na_m] <- 0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3018
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3019 tmp <- m[, 0 < colSums(x = tmp)] # by default, na.rm is FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3020
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3021 colnames_tmp <- colnames(tmp)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3022
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3023 my_low_p_seq <- seq(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3024 from = min(g_intensity_hm_rows, nrow(m)),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3025 to = 1,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3026 by = -1
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3027 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3028
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3029 if (g_correlate_substrates) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3030 # zap samples having zero or near-zero variance
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3031 tmp[is.na(tmp)] <- 0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3032 nzv <- caret::nearZeroVar(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3033 tmp, # matrix of values, samples x variables
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3034 freqCut = 1.01, # min(freq most prevalent value /
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3035 # freq second most prevalent)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3036 uniqueCut = 99 # max(number of unique values /
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3037 # total number of samples)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3038 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3039 tmp <- if (length(nzv) > 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3040 m[, -nzv, drop = FALSE]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3041 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3042 m
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3043 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3044 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3045 tmp <- m[my_low_p_seq, , drop = FALSE]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3046 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3047
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3048
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3049 t_m <- t(tmp)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3050 t_m[is.na(t_m)] <- 0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3051 prefiltered_nrow <- ncol(t_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3052
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3053 my_corcov <- cov(t_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3054 did_filter_rows <- did_filter_cols <- FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3055 if (g_correlate_substrates && !is_positive_definite(my_corcov)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3056 my_correlate_substrates <- FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3057 t_m <- t(m[my_low_p_seq, , drop = FALSE])
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3058 t_m[is.na(t_m)] <- 0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3059 unfiltered_row_count <- ncol(t_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3060 unfiltered_col_count <- nrow(t_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3061
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3062 # zap empty samples
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3063 t_m <- t_m[0 < rowSums(x = t_m), ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3064 # zap substrates present in fewer than two samples
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3065 foo <- t_m > 0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3066 foo <- colSums(x = foo) > 1
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3067 t_m <- t_m[, foo]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3068
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3069 did_filter_rows <- unfiltered_row_count > ncol(t_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3070 did_filter_cols <- unfiltered_col_count > nrow(t_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3071
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3072 colnames_tmp <- rownames(t_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3073 my_corcov <- cov(t_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3074 if (g_filter_cov_var_gt_1) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3075 my_corcov <- keep_cov_w_var_gtr_1(my_corcov)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3076 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3077 } else if (g_correlate_substrates) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3078 my_corcov <- cov2cor(my_corcov)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3079 my_correlate_substrates <- TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3080 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3081 my_correlate_substrates <- FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3082 if (g_filter_cov_var_gt_1) my_corcov <- keep_cov_w_var_gtr_1(my_corcov)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3083 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3084
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3085 omitted_samples <- colnames_m[colnames_m %notin% colnames_tmp]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3086 suffix <- if (length(omitted_samples) > 1) "s" else ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3087
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3088 f_omissions <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3089 function(is_corr) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3090 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3091 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3092 "Below is the %s plot for %s substrates",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3093 if (is_corr) "correlation" else "covariance",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3094 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3095 if (top_substrates)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3096 "%0.0f \"highest-quality\""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3097 else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3098 "%0.0f",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3099 ncol(t_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3100 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3101 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3102 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3103 if (did_filter_cols) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3104 cat(sprintf(", omitting sample%s ", suffix))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3105 latex_collapsed_vector(", ", omitted_samples)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3106 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3107 cat(".\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3108 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3109
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3110 if (is.null(my_corcov) || sum(!is.na(t_m)) < 2) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3111 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3112 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3113 "\\newline\n%s %s plot.\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3114 "Insufficient covariance to produce",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3115 if (my_correlate_substrates)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3116 "correlation"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3117 else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3118 "covariance"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3119 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3120 "\\newpage\n"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3121 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3122 return(NULL)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3123 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3124
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3125 cat("\\leavevmode\n", "\\newpage\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3126 f_omissions(my_correlate_substrates)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3127
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3128 master_cex <- 0.4
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3129 max_nchar <- max(nchar(rownames(t_m)))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3130 my_limit <- g_intensity_hm_rows
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3131 diminution <- sqrt(my_limit / (my_limit + ncol(t_m)))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3132 my_row_cex <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3133 my_col_cex <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3134 min(1.75, master_cex * 9 * diminution ^ 1.5)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3135 my_margin <- 3 + my_row_cex * 64 / (8 + max_nchar)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3136 my_key_cex <- 1.4
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3137 my_hm2_cex <- 1.0 * master_cex
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3138 my_hgt_scale <- 3.50 - 0.26 * (max(0.4, my_key_cex) - 0.4)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3139 my_hgt_scale <- 2.7
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3140
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3141 my_legend_height <- 4.0 - my_hgt_scale
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3142 my_legend_height <- 0.5 * my_key_cex
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3143 my_warp <- 0.65 * (my_limit + ncol(t_m)) / my_limit
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3144 my_warp <- 0.8
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3145 my_legend_height <- 0.77
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3146 my_legend_height <- 0.67
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3147 my_plot_height <- my_hgt_scale + (1 - my_warp) * my_legend_height
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3148 my_legend_height <- my_warp * my_legend_height
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3149
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3150 parjust <- par(adj = 0.5)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3151 on.exit(par(parjust))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3152 my_corcov <- my_corcov[order(rownames(my_corcov)), ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3153 my_main <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3154 sprintf("%s among %s substrates %s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3155 if (my_correlate_substrates) "Correlation"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3156 else "Covariance",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3157 kinase_name,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3158 if (!my_correlate_substrates &&
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3159 g_filter_cov_var_gt_1 &&
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3160 did_filter_rows
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3161 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3162 "having variance > 1"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3163 else ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3164 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3165 my_main_nchar <- nchar(my_main)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3166 my_heights <- c(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3167 0.3,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3168 my_plot_height,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3169 my_legend_height # was 4.0 - my_hgt_scale # was 4.19
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3170 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3171 if (print_trace_messages) cat(sprintf("max_nchar = %0.3f; ", max_nchar))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3172 if (print_trace_messages) cat(sprintf("my_margin = %0.3f; ", my_margin))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3173 if (print_trace_messages) cat(sprintf("my_plot_height = %0.3f\n\n", my_plot_height))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3174 if (print_trace_messages) cat(sprintf("master_cex = %0.3f; ", master_cex))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3175 if (print_trace_messages) cat(sprintf("my_row_cex = %0.3f; ", my_row_cex))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3176 if (print_trace_messages) cat(sprintf("my_col_cex = %0.3f; ", my_col_cex))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3177 if (print_trace_messages) cat(sprintf("my_key_cex = %0.3f\n\n", my_key_cex))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3178 if (print_trace_messages) cat(sprintf("my_hgt_scale = %0.3f\n\n", my_hgt_scale))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3179 if (print_trace_messages) cat(sprintf("legend height = %0.3f\n\n", my_legend_height))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3180 if (print_trace_messages) cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3181 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3182 "my_heights = c(%s); sum = %0.3f\n\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3183 paste(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3184 sprintf("%0.3f", my_heights),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3185 collapse = ", "
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3186 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3187 sum(my_heights)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3188 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3189 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3190 op <- par(cex.main = (30 + my_main_nchar) / my_main_nchar)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3191 on.exit(par(op))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3192 hm2plus(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3193 x = my_corcov,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3194 cex = my_hm2_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3195 cexCol = my_col_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3196 cexRow = my_row_cex,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3197 density_info = "none",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3198 denhgt = 0.15,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3199 denwid = 0.5,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3200 divergent = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3201 key_par = list(cex = my_key_cex),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3202 key_xlab = if (my_correlate_substrates) "Correlation"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3203 else "Covariance",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3204 main = my_main,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3205 mat = matrix(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3206 c(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3207 c(0, 3, 3),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3208 c(2, 1, 1),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3209 c(0, 4, 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3210 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3211 nrow = 3,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3212 ncol = 3,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3213 byrow = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3214 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3215 heights = my_heights,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3216 margins = c(my_margin, my_margin),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3217 widths = c(0.5, 3.1, 0.9),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3218 scale = "none",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3219 symkey = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3220 symbreaks = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3221 symm = FALSE #TODO evaluate TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3222 # ...
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3223 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3224 } # end cov_heatmap
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3225
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3226 ### FILE IMPORT
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3227
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3228 # function reading bzipped file to data.frame
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3229 bzip2df <- function(d, f, ctor = bzfile) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3230 # read.delim file (by default, compressed by bzip2)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3231 if (file.exists(f)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3232 conn <- NULL
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3233 pf <- parent.frame()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3234 tryCatch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3235 assign(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3236 as.character(substitute(d)),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3237 read.delim(conn <- bzfile(f, open = "r")),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3238 pf
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3239 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3240 finally = if (!is.null(conn)) close(conn)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3241 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3242 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3243 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3244
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3245 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3246
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
3247 # Purpose
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
3248
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3249 The purpose of this analysis is to perform for phosphopeptides:
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3250
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3251 - imputation of missing values,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3252 - quantile normalization,
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3253 - ANOVA (using the R stats::`r params$oneWayManyCategories` function),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3254 - assignment of an FDR-adjusted $p$-value and a "quality score" to each phosphopeptide, and
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3255 - KSEA (Kinase-Substrate Enrichment Analysis) using code adapted from the CRAN `KSEAapp` package to search for kinase substrates from the following databases:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3256 - PhosphoSitesPlus [https://www.phosphosite.org](https://www.phosphosite.org)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3257 - The Human Proteome Database [http://hprd.org](http://hprd.org)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3258 - NetworKIN [http://networkin.science/](http://networkin.science/)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3259 - Phosida [http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx](http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3260
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3261 ```{r include = FALSE}
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3262
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3263 if (params$kseaUseAbsoluteLog2FC) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3264 sfc <- "|s|"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3265 pfc <- "|p|"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3266 pfc_txt <- "$\\text{absolute value}({\\log_2 (\\text{fold-change})})$"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3267 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3268 sfc <- "s"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3269 pfc <- "p"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3270 pfc_txt <- "${\\log_2 (\\text{fold-change}})$"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3271 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3272
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3273 ksea_heatmap_titles <- list()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3274 ksea_heatmap_titles[[const_ksea_astrsk_kinases]] <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3275 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3276 "Summary for all kinases enriched in one or more contrasts at %s < %s",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3277 ksea_cutoff_statistic,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3278 ksea_cutoff_threshold
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3279 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3280 ksea_heatmap_titles[[const_ksea_all_kinases]] <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3281 "Summary figure for all contrasts and all kinases"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3282 ksea_heatmap_titles[[const_ksea_nonastrsk_kinases]] <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3283 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3284 "Summary for all kinases not enriched at %s < %s in any contrast",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3285 ksea_cutoff_statistic,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3286 ksea_cutoff_threshold
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3287 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
3288 # hash to hold names of significantly enriched kinases
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3289 ksea_asterisk_hash <- new_env()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
3290
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
3291 # PROCESS (mostly read) PARAMETERS
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
3292
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
3293 # False discovery rate adjustment for ANOVA
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
3294 # Since pY abundance is low, set to 0.10 and 0.20 in addition to 0.05
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3295 val_fdr <- read.table(file = alpha_file, sep = "\t", header = FALSE, quote = "")
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3296
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3297 if (
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3298 ncol(val_fdr) != 1 ||
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3299 sum(!is.numeric(val_fdr[, 1])) ||
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3300 sum(val_fdr[, 1] < 0) ||
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3301 sum(val_fdr[, 1] > 1)
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3302 ) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3303 cat("alphaFile should be one column of numbers within the range [0.0,1.0]")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3304 param_df_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3305 knitr::knit_exit()
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3306 }
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3307 val_fdr <- val_fdr[, 1]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3308
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3309 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3310
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3311 ```{r echo = FALSE, results = 'asis'}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3312
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3313
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3314 result <- file.copy(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3315 from = preproc_db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3316 to = ksea_app_prep_db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3317 overwrite = TRUE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3318 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3319 if (!result) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3320 write(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3321 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3322 "fatal error copying initial database '%s' to output '%s'",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3323 preproc_db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3324 ksea_app_prep_db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3325 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3326 stderr()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3327 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3328 if (sys.nframe() > 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3329 cat("Cannot continue and quit() failed. Goodbye.")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3330 param_df_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3331 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3332 # in case knit_exit doesn't exit
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3333 quit(save = "no", status = 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3334 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3335 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3336
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3337 if (FALSE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3338 write.table(x = param_df, file = "test-data/params.txt")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3339 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3340
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3341 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3342
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3343 ```{r echo = FALSE}
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3344 ### READ DATA
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3345
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3346 # read.table reads a file in table format and creates a data frame from it.
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3347 # - note that `quote = ""` means that quotation marks are treated literally.
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3348 full_data <- read.table(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3349 file = input_file,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3350 sep = "\t",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3351 header = TRUE,
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3352 quote = "",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3353 check.names = FALSE
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3354 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3355
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3356 ```
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3357
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3358
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3359 # Extraction of Sample Classes and Names from Input Data
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3360
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3361 ```{r echo = FALSE, results = 'asis'}
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3362
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3363 data_column_indices <- grep(first_data_column, names(full_data), perl = TRUE)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3364 my_column_names <- names(full_data)
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3365
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3366 if (!fdc_is_integer) {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3367 if (length(data_column_indices) > 0) {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3368 first_data_column <- data_column_indices[1]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3369 } else {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3370 cat(paste("failed to convert firstDataColumn:", first_data_column))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3371 param_df_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3372 knitr::knit_exit()
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3373 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3374 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3375
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3376 cat(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3377 sprintf(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3378 paste(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3379 "\n\nThe input data file has peptide-intensity data",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3380 "in columns %d (\"%s\") through %d (\"%s\")."
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3381 ),
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3382 tmp <- min(data_column_indices),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3383 my_column_names[tmp],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3384 tmp <- max(data_column_indices),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3385 my_column_names[tmp]
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3386 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3387 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3388
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3389 if (TRUE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3390 cat0(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3391 table_offset(i = 1, new = TRUE),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3392 "Sample classes and names are shown in ",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3393 table_href(),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3394 ".\n\n"
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3395 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3396 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3397 cat0(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3398 "\\newcounter{offset}\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3399 "\\setcounter{offset}{\\value{table}}\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3400 "\\stepcounter{offset}\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3401 "Sample classes and names are shown in ",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3402 table_href(),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3403 ".\n\n"
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3404 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3405 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3406
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3407 #TODO remove this unused variable and assignment
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3408 if (FALSE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3409 # Write column names as a LaTeX enumerated list.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3410 column_name_df <- data.frame(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3411 column = seq_len(length(colnames(full_data))),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3412 name = paste0("\\verb@", colnames(full_data), "@")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3413 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3414 }
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3415
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3416 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3417
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3418 ```{r echo = FALSE, results = 'asis'}
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3419 # extract intensity columns from full_data to quant_data
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3420 quant_data <- full_data[first_data_column:length(full_data)]
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3421 quant_data[quant_data == 0] <- NA
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3422 rownames(quant_data) <- rownames(full_data) <- full_data$Phosphopeptide
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3423 full_data_names <- colnames(quant_data)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3424 # Extract factors and trt-replicates using regular expressions.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3425 # Typically:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3426 # regex_sample_names is "\\.\\d+[A-Z]$"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3427 # regex_sample_grouping is "\\d+"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3428 # This would distinguish trt-replicates by terminal letter [A-Z]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3429 # in sample names and group them into trts by the preceding digits.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3430 # e.g.:
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3431 # group .1A .1B .1C into group 1;
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3432 # group .2A .2B .2C, into group 2;
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3433 # etc.
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3434 m <- regexpr(regex_sample_names, colnames(quant_data), perl = TRUE)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3435 sample_name_matches <- regmatches(names(quant_data), m)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3436 colnames(quant_data) <- sample_name_matches
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3437
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3438 write_debug_file(quant_data)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3439
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3440 rx_match <- regexpr(regex_sample_grouping, sample_name_matches, perl = TRUE)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3441 smpl_trt <- as.factor(regmatches(sample_name_matches, rx_match))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3442
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3443 if (print_nb_messages) nbe(see_variable(smpl_trt, "\n\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3444 if (print_nb_messages) nbe(see_variable(sample_name_matches, "\n\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3445 if (print_nb_messages) nbe(see_variable(full_data_names, "\n\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3446
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3447 sample_treatment_df <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3448 save_sample_treatment_df <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3449 data.frame(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3450 class = smpl_trt,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3451 sample = sample_name_matches,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3452 full_sample_names = full_data_names
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3453 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3454
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3455 if (print_nb_messages) nbe(see_variable(sample_treatment_df, "\n\n"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3456
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3457 # reorder data
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3458 my_order <- with(sample_treatment_df, order(class, sample))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3459 quant_data <- quant_data[, my_order]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3460 sample_name_matches <- sample_name_matches[my_order]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3461 smpl_trt <- smpl_trt[my_order]
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3462 sample_treatment_df <- data.frame(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3463 class = smpl_trt,
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3464 sample = sample_name_matches
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3465 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3466
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3467 # filter smpl_trt as appropriate
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3468 if (sample_group_filter %in% c("include", "exclude")) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3469 include_sample <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3470 mgrepl(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3471 v = sample_group_filter_patterns,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3472 s = as.character(smpl_trt),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3473 fixed = sample_group_filter_fixed,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3474 perl = sample_group_filter_perl,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3475 ignore.case = sample_group_filter_nocase
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3476 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3477 if (sum(include_sample) < 2) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3478 errmsg <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3479 paste(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3480 "ERROR:",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3481 sum(include_sample),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3482 "samples are too few for analysis;",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3483 "check input parameters for sample-name parsing"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3484 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3485 cat0(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3486 errmsg,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3487 "\\stepcounter{offset}\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3488 " in ",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3489 table_href(),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3490 ".\n\n"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3491 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3492 data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3493 x = save_sample_treatment_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3494 tabstops = c(1.25, 1.25),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3495 caption = "Sample classes",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3496 use_subsubsection_header = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3497 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3498 data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3499 x =
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3500 param_df[
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3501 c("regexSampleNames",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3502 "regexSampleGrouping",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3503 "groupFilterPatterns",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3504 "groupFilter",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3505 "groupFilterMode"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3506 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3507 ],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3508 tabstops = c(1.75),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3509 underscore_whack = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3510 caption = "Input parameters for sample-name parsing",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3511 verbatim = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3512 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3513 param_df_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3514 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3515 return(invisible(-1))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3516 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3517 sample_treatment_df <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3518 if (sample_group_filter == "include")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3519 sample_treatment_df[include_sample, ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3520 else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3521 sample_treatment_df[!include_sample, ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3522 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3523 include_sample <- rep.int(TRUE, length(smpl_trt))
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3524 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3525 sample_name_matches <- sample_treatment_df$sample
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3526 rx_match <- regexpr(regex_sample_grouping, sample_name_matches, perl = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3527 smpl_trt <- as.factor(regmatches(sample_name_matches, rx_match))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3528 sample_treatment_df$class <- smpl_trt
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3529
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3530 # filter quant_data as appropriate
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3531 number_of_samples <- length(sample_name_matches)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3532 quant_data <- quant_data[, sample_name_matches]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3533
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3534 sample_level_integers <- as.integer(smpl_trt)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3535 sample_treatment_levels <- levels(smpl_trt)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3536 count_of_treatment_levels <- length(sample_treatment_levels)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3537
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3538 # for each phosphopeptide, across treatment levels, compute minimum
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3539 # count of observed (i.e., non-missing) values
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3540 my_env <- new_env()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3541 for (l in sample_treatment_levels)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3542 my_env[[as.character(l)]] <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
3543 as.vector(rowSums(!is.na(quant_data[l == smpl_trt])))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3544 min_group_obs_count <- row_apply(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3545 x = Reduce(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3546 f = function(l, r) cbind(l, my_env[[r]]),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3547 x = sample_treatment_levels,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3548 init = c()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3549 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3550 fun = min
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3551 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3552 names(min_group_obs_count) <- rownames(quant_data)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3553 rm(my_env)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3554
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3555 # display (possibly-filtered) results
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3556 cat("\\newpage\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3557
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3558 if (sum(include_sample) > 1) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3559 data_frame_tabbing_latex(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3560 x = sample_treatment_df,
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3561 tabstops = c(1.25),
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3562 caption = "Sample classes",
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3563 use_subsubsection_header = FALSE
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3564 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3565 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3566 sample_name_grow <- 10 / (10 + max(nchar(sample_name_matches) + 6))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3567 sample_colsep <- transition_positions(as.integer(sample_treatment_df$class))
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3568 ```
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3569
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3570 ```{r echo = FALSE, results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3571 cat("\\newpage\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3572 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3573
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3574 ## Are the log-transformed sample distributions similar?
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3575
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3576 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'}
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3577
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3578 quant_data[quant_data == 0] <- NA #replace 0 with NA
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3579 quant_data_log <- log10(quant_data)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3580
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3581 rownames(quant_data_log) <- rownames(quant_data)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3582 colnames(quant_data_log) <- sample_name_matches
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3583
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3584 write_debug_file(quant_data_log)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3585
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3586 g_ppep_distrib_ctl <- new_env()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3587 g_ppep_distrib_ctl$xlab_line <- 3.5 + 11.86 * (0.67 - sample_name_grow)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3588 g_ppep_distrib_ctl$mai_bottom <- (0.5 + 3.95 * (0.67 - sample_name_grow))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3589 g_ppep_distrib_ctl$axis <- (0.6 + 0.925 * (0.67 - sample_name_grow))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3590
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3591 my_ppep_distrib_bxp <- function(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3592 x
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3593 , sample_name_grow = sample_name_grow
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3594 , main
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3595 , varwidth = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3596 , sub = NULL
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3597 , xlab
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3598 , ylab
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3599 , col = const_boxplot_fill
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3600 , notch = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3601 , ppep_distrib_ctl = g_ppep_distrib_ctl
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3602 , ...
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3603 ) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3604 my_xlab_line <- g_ppep_distrib_ctl$xlab_line
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3605 my_mai_bottom <- g_ppep_distrib_ctl$mai_bottom
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3606 my_axis <- g_ppep_distrib_ctl$axis
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3607
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3608 if (print_trace_messages) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3609 cat_variable(my_xlab_line, suffix = "; ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3610 cat_variable(my_mai_bottom, suffix = "; ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3611 cat_variable(my_axis, suffix = "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3612 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3613
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3614 old_par <- par(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3615 mai = par("mai") + c(my_mai_bottom, 0, 0, 0),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3616 cex.axis = my_axis,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3617 cex.lab = 1.2
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3618 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3619 tryCatch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3620 {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3621 # Vertical plot
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3622 boxplot(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3623 x
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3624 , las = 2
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3625 , col = col
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3626 , main = main
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3627 , sub = NULL
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3628 , ylab = ylab
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3629 , xlab = NULL
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3630 , notch = notch
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3631 , varwidth = varwidth
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3632 , ...
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3633 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3634 title(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3635 sub = sub
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3636 , cex.sub = 1.0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3637 , line = my_xlab_line + 1
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3638 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3639 title(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3640 xlab = xlab
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3641 , line = my_xlab_line
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3642 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3643 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3644 finally = par(old_par)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3645 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3646 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3647
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3648 my_ppep_distrib_bxp(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3649 x = quant_data_log
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3650 , sample_name_grow = sample_name_grow
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3651 , main = "Peptide intensities for each sample"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3652 , varwidth = boxplot_varwidth
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3653 , sub = "Box widths reflect number of peptides for sample"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3654 , xlab = "Sample"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3655 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3656 , col = const_boxplot_fill
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3657 , notch = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3658 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3659
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3660 cat("\n\n\n\n")
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3661
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3662 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3663
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3664 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3665 if (nrow(quant_data_log) > 1) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3666 quant_data_log_stack <- stack(quant_data_log)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3667 ggplot2::ggplot(quant_data_log_stack, ggplot2::aes(x = values)) +
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3668 ggplot2::xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) +
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3669 ggplot2::ylab("Probability density") +
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3670 ggplot2::geom_density(ggplot2::aes(group = ind, colour = ind), na.rm = TRUE)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3671 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3672 cat("No density plot because there are too few peptides.\n\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3673 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3674 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3675
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3676 ## Globally, are peptide intensities are approximately unimodal?
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3677
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3678 <!--
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3679 # bquote could be used as an alternative to latex2exp::TeX below particularly
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3680 # and when plotting math expressions generally, at the expense of mastering
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3681 # another syntax, which hardly seems worthwhile when I need to use TeX
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3682 # elsewhere; here's an introduction to bquote:
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3683 # https://www.r-bloggers.com/2018/03/math-notation-for-r-plot-titles-expression-and-bquote/
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3684 -->
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3685 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'}
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3686
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3687 # identify the location of missing values
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3688 fin <- is.finite(as.numeric(as.matrix(quant_data_log)))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3689
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3690 logvalues <- as.numeric(as.matrix(quant_data_log))[fin]
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3691 logvalues_density <- density(logvalues)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3692 plot(
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3693 x = logvalues_density,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3694 main = latex2exp::TeX(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3695 "Smoothed estimated probability density vs. $log_{10}$(peptide intensity)"
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3696 ),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3697 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3698 ylab = "Probability density"
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3699 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3700 hist(
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3701 x = as.numeric(as.matrix(quant_data_log)),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3702 xlim = c(min(logvalues_density$x), max(logvalues_density$x)),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3703 breaks = 100,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3704 main = latex2exp::TeX("Frequency vs. $log_{10}$(peptide intensity)"),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3705 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3706 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3707 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3708
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3709 # Characterization of Input Data
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3710
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3711 ## Distribution of standard deviations of $log_{10}(\text{intensity})$, ignoring missing values
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3712
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3713 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'}
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3714 # determine quantile
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3715 q1 <- quantile(logvalues, probs = mean_percentile)[1]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3716
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3717 # 1 = row of matrix (ie, phosphopeptide)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3718 sds <- row_apply(quant_data_log, sd_finite)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3719 if (sum(!is.na(sds)) > 2) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3720 plot(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3721 density(sds, na.rm = TRUE)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3722 , main = "Smoothed estimated probability density vs. std. deviation"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3723 , sub = "(probability estimation made with Gaussian smoothing)"
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3724 , ylab = "Probability density"
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3725 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3726 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3727 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3728 "At least two non-missing values are required to plot",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3729 "probability density.\n\n"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3730 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3731 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3732
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3733 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3734
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3735 ```{r echo = FALSE}
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3736 # Determine number of cells to impute
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3737 temp <- quant_data[is.na(quant_data)]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3738
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3739 # Determine number of values to impute
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3740 number_to_impute <- length(temp)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3741
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3742 # Determine percent of missing values
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3743 pct_missing_values <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3744 round(length(temp) / (length(logvalues) + length(temp)) * 100)
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3745 ```
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3746
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3747 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3748
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3749 # prep for trt-median based imputation
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3750
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3751 ```
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3752 # Imputation of Missing Values
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3753
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3754 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3755
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3756 imp_smry_pot_peptides_before <- nrow(quant_data_log)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3757 imp_smry_missing_values_before <- number_to_impute
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3758 imp_smry_pct_missing <- pct_missing_values
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3759
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3760 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3761
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3762 ```{r echo = FALSE}
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3763 #Determine number of cells to impute
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3764
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3765 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3766 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3767
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3768 # Identify which values are missing and need to be imputed
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3769 ind <- which(is.na(quant_data), arr.ind = TRUE)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3770
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3771 ```
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3772 ```{r echo = FALSE, results = 'asis'}
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3773
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3774 # Apply imputation
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3775 switch(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3776 imputation_method
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3777 , "group-median" = {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3778 quant_data_imp <- quant_data
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3779 imputation_method_description <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3780 paste("Substitute missing value with",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3781 "median peptide-intensity for sample group.\n"
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3782 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3783 # Take the accurate ln(x+1) because the data are log-normally distributed
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3784 # and because median can involve an average of two measurements.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3785 quant_data_imp <- log1p(quant_data_imp)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3786 for (i in seq_len(count_of_treatment_levels)) {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3787 # Determine the columns for this factor-level
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3788 level_cols <- i == sample_level_integers
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3789 # Extract those columns
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3790 lvlsbst <- quant_data_imp[, level_cols, drop = FALSE]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3791 # assign to ind the row-column pairs corresponding to each NA
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3792 ind <- which(is.na(lvlsbst), arr.ind = TRUE)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3793 # No group-median exists if there is only one sample
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3794 # a given ppep has no measurement; otherwise, proceed.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3795 if (ncol(lvlsbst) > 1) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3796 the_centers <-
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3797 row_apply(lvlsbst, median, na.rm = TRUE)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3798 for (j in seq_len(nrow(lvlsbst))) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3799 for (k in seq_len(ncol(lvlsbst))) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3800 if (is.na(lvlsbst[j, k])) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3801 lvlsbst[j, k] <- the_centers[j]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3802 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3803 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3804 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3805 quant_data_imp[, level_cols] <- lvlsbst
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3806 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3807 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3808 # Take the accurate e^x - 1 to match scaling of original input.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3809 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp))
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3810 good_rows <- !is.na(rowMeans(quant_data_imp))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3811 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3812 , "median" = {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3813 quant_data_imp <- quant_data
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3814 imputation_method_description <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3815 paste("Substitute missing value with",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3816 "median peptide-intensity across all sample classes.\n"
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3817 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3818 # Take the accurate ln(x+1) because the data are log-normally distributed
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3819 # and because median can involve an average of two measurements.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3820 quant_data_imp <- log1p(quant_data_imp)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3821 quant_data_imp[ind] <- row_apply(quant_data_imp, median, na.rm = TRUE)[ind[, 1]]
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3822 # Take the accurate e^x - 1 to match scaling of original input.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3823 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3824 good_rows <- !is.nan(rowMeans(quant_data_imp))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3825 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3826 , "mean" = {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3827 quant_data_imp <- quant_data
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3828 imputation_method_description <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3829 paste("Substitute missing value with",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3830 "geometric-mean peptide intensity across all sample classes.\n"
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3831 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3832 # Take the accurate ln(x+1) because the data are log-normally distributed,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3833 # so arguments to mean should be previously transformed.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3834 # this will have to be
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3835 quant_data_imp <- log1p(quant_data_imp)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3836 # Assign to NA cells the mean for the row
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3837 quant_data_imp[ind] <- row_apply(quant_data_imp, mean, na.rm = TRUE)[ind[, 1]]
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3838 # Take the accurate e^x - 1 to match scaling of original input.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3839 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3840 good_rows <- !is.nan(rowMeans(quant_data_imp))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3841 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3842 , "random" = {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3843 quant_data_imp <- quant_data
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3844 m1 <- median(sds, na.rm = TRUE) * sd_percentile #sd to be used is the median sd
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3845 # If you want results to be reproducible, you will want to call
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3846 # base::set.seed before calling stats::rnorm
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3847 imputation_method_description <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3848 paste("Substitute each missing value with random intensity",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3849 sprintf(
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
3850 "random intensity $N \\sim (%0.2f, %0.2f)$.\n",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3851 q1, m1
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3852 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3853 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3854 cat(sprintf("mean_percentile (from input parameter) is %2.0f\n\n",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3855 100 * mean_percentile))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3856 cat(sprintf("sd_percentile (from input parameter) is %0.2f\n\n",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3857 sd_percentile))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3858 quant_data_imp[ind] <-
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3859 10 ^ rnorm(number_to_impute, mean = q1, sd = m1)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3860 quant_data_imp_ln <- log1p(quant_data_imp)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3861 good_rows <- !is.nan(rowMeans(quant_data_imp))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3862 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3863 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3864 quant_data_imp_log10 <- quant_data_imp_ln * const_log10_e
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3865
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3866 if (length(good_rows) < 1) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3867 print("ERROR: Cannot impute data; there are no good rows!")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3868 return(-1)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3869 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3870 ```
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3871
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3872 ```{r echo = FALSE, results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3873 cat("\\quad\n\nImputation method:\n\n\n", imputation_method_description)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3874 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3875
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3876 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3877
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3878 imp_smry_pot_peptides_after <- sum(good_rows)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3879 imp_smry_rejected_after <- sum(!good_rows)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3880 imp_smry_missing_values_after <- sum(is.na(quant_data_imp[good_rows, ]))
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3881
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3882 # From ?`%in%`, %in% is currently defined as function(x, table) match(x, table, nomatch = 0) > 0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3883
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3884 sink(stderr())
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3885 print("`%in%`:")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3886 print(`%in%`)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3887 sink()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3888
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3889 stock_in <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3890 names(good_rows) %in%
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3891 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count])
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3892 if (print_nb_messages) nbe(see_variable(stock_in), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3893
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3894 explicit_in <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3895 0 < match(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3896 names(good_rows),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3897 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count])
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3898 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3899 if (print_nb_messages) nbe(see_variable(explicit_in), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3900
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3901 great_enough_row_names <- good_rows[
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3902 names(good_rows) %in%
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3903 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count])
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3904 ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3905 if (print_nb_messages) nbe(see_variable(great_enough_row_names), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3906 great_enough_row_names <- great_enough_row_names[great_enough_row_names]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3907 if (print_nb_messages) nbe(see_variable(great_enough_row_names), "\n")
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3908 ```
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3909
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3910 ```{r echo = FALSE, results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3911 # ref: http://www1.maths.leeds.ac.uk/latex/TableHelp1.pdf
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3912 tabular_lines_fmt <- paste(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3913 "\\begin{table}[hb]", # h(inline); b(bottom); t (top) or p (separate page)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3914 " \\leavevmode",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3915 " \\caption{Imputation Results}",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3916 " \\centering", # \centering centers the table on the page
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3917 " \\begin{tabular}{l c c c}",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3918 " \\hline\\hline",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3919 " \\ & potential peptides & missing values & rejected",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3920 " peptides \\\\ [0.5ex]",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3921 " \\hline",
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3922 " before imputation & %d & %d (%d\\%s) & \\\\",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3923 " after imputation & %d & %d & %d \\\\",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3924 " after keep comparable & %d & & %d \\\\ [1ex]",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3925 " \\hline",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3926 " \\end{tabular}",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3927 #" \\label{table:nonlin}", # may be used to refer this table in the text
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3928 "\\end{table}",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3929 sep = "\n"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3930 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3931 tabular_lines <-
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3932 sprintf(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3933 tabular_lines_fmt,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3934 imp_smry_pot_peptides_before,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3935 imp_smry_missing_values_before,
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3936 imp_smry_pct_missing,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3937 "%",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3938 imp_smry_pot_peptides_after,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3939 imp_smry_missing_values_after,
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3940 imp_smry_rejected_after,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3941 length(great_enough_row_names),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3942 imp_smry_pot_peptides_before -
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3943 length(great_enough_row_names)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3944 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3945 cat(tabular_lines)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3946 ```
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3947
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3948 ```{r filter_good_rows, echo = FALSE}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3949
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3950 if (print_nb_messages) nbe("before name extraction, ", see_variable(length(good_rows)), " ", see_variable(good_rows), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3951 good_rows <- names(good_rows[names(great_enough_row_names)])
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3952 if (print_nb_messages) nbe("after name extraction, ", see_variable(length(good_rows)), see_variable(good_rows), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3953
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3954 #ACE min_group_obs_count <- min_group_obs_count[names(great_enough_row_names)]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3955 #ACE nbe("good_rows")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3956 #ACE nbe(see_variable(good_rows))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3957 #ACE nbe("names(min_group_obs_count) before filter for good rows")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3958 #ACE nbe(see_variable(names(min_group_obs_count)))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3959 min_group_obs_count <- min_group_obs_count[good_rows]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3960 #ACE nbe("min_group_obs_count after filter for good rows")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3961 #ACE nbe(see_variable(names(min_group_obs_count)))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3962
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3963 # Zap rows where imputation was insufficiently effective
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3964 full_data <- full_data [good_rows, ]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3965 quant_data <- quant_data [good_rows, ]
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3966 quant_data_log <- quant_data_log [good_rows, ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3967
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3968 if (print_nb_messages) nbe("before row filter, ", see_variable(nrow(quant_data_imp)), "\n")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3969 quant_data_imp <- quant_data_imp[good_rows, ]
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
3970 if (print_nb_messages) nbe("after row filter, ", see_variable(nrow(quant_data_imp)), "\n")
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3971 write_debug_file(quant_data_imp)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3972 quant_data_imp_good_rows <- quant_data_imp
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3973
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3974 write_debug_file(quant_data_imp_good_rows)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3975 ```
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3976
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3977 ```{r echo = FALSE, results = 'asis'}
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3978
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3979 can_plot_before_after_imp <- TRUE
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3980 d_combined <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3981 as.numeric(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3982 as.matrix(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3983 log10(quant_data_imp)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3984 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3985 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
3986 d_original <-
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3987 as.numeric(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3988 as.matrix(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3989 log10(quant_data_imp[!is.na(quant_data)])
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3990 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3991 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
3992
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3993 if (sum(!is.na(d_original)) > 2) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3994 d_original <- density(d_original)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3995 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3996 can_plot_before_after_imp <- FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3997 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3998 if (can_plot_before_after_imp && sum(is.na(d_combined)) < 1) {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
3999 d_combined <- density(d_combined)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4000 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4001 can_plot_before_after_imp <- FALSE
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4002 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4003
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4004 if (sum(is.na(quant_data)) > 0) {
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4005 # There ARE missing values
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4006 d_imputed <-
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4007 as.numeric(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4008 as.matrix(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4009 log10(quant_data_imp[is.na(quant_data)])
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4010 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4011 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4012 if (can_plot_before_after_imp && sum(is.na(d_imputed)) < 1) {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4013 d_imputed <- (density(d_imputed))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4014 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4015 can_plot_before_after_imp <- FALSE
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4016 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4017 } else {
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4018 # There are NO missing values
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4019 d_imputed <- d_combined
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4020 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4021
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4022 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4023
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4024 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'}
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4025 zero_sd_rownames <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4026 rownames(quant_data_imp)[
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4027 is.na((row_apply(quant_data_imp, sd, na.rm = TRUE)) == 0)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4028 ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4029
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4030 if (length(zero_sd_rownames) >= nrow(quant_data_imp)) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4031 cat("All peptides have zero standard deviation. Cannot continue.")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4032 param_df_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4033 knitr::knit_exit()
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4034 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4035 if (length(zero_sd_rownames) > 0) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4036 cat(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4037 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4038 "%d %s %s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4039 length(zero_sd_rownames),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4040 "peptides with zero variance",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4041 "were removed from statistical consideration"
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4042 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4043 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4044 zap_named_rows <- function(df, nms) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4045 return(df[!(row.names(df) %in% nms), ])
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4046 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4047 quant_data_imp <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4048 zap_named_rows(quant_data_imp, zero_sd_rownames)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4049 quant_data <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4050 zap_named_rows(quant_data, zero_sd_rownames)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4051 full_data <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4052 zap_named_rows(full_data, zero_sd_rownames)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4053 min_group_obs_count <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4054 min_group_obs_count[names(min_group_obs_count) %notin% zero_sd_rownames]
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4055 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4056
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4057 if (sum(is.na(quant_data)) > 0) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4058 cat("\\leavevmode\\newpage\n")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4059 # Copy quant data to x
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4060 x <- quant_data
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4061 # x gets to have values of:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4062 # - NA for observed values
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4063 # - 1 for missing values
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4064 x[is.na(x)] <- 0
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4065 x[x > 1] <- NA
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4066 x[x == 0] <- 1
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4067 # Log-transform imputed data
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4068 # update variable because rows may have been eliminated from quant_data_imp
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4069 quant_data_imp_log10 <- log10(quant_data_imp)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4070
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4071 write_debug_file(quant_data_imp_log10)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4072
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4073 # Set blue_dots to log of quant data or NA for NA quant data
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4074 blue_dots <- log10(quant_data)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4075 # Set red_dots to log of imputed data or NA for observed quant data
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4076 red_dots <- quant_data_imp_log10 * x
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4077
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4078 count_red <- sum(!is.na(red_dots))
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4079 count_blue <- sum(!is.na(blue_dots))
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4080 ylim_save <- ylim <- c(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4081 min(red_dots, blue_dots, na.rm = TRUE),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4082 max(red_dots, blue_dots, na.rm = TRUE)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4083 )
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4084 show_stripchart <-
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4085 50 > (count_red + count_blue) / length(sample_name_matches)
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4086 if (show_stripchart) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4087 boxplot_sub <- "Light blue = data before imputation; Red = imputed data;"
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4088 } else {
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4089 boxplot_sub <- ""
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4090 }
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4091
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4092 # Vertical plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4093 colnames(blue_dots) <- sample_name_matches
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4094 my_ppep_distrib_bxp(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4095 x = blue_dots
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4096 , sample_name_grow = sample_name_grow
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4097 , main = "Peptide intensities after eliminating unusable peptides"
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4098 , varwidth = boxplot_varwidth
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4099 , sub = paste(boxplot_sub, "Box widths reflect number of peptides for sample")
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4100 , xlab = "Sample"
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4101 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4102 , col = const_boxplot_fill
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4103 , notch = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4104 , ylim = ylim
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4105 )
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4106
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4107 if (show_stripchart) {
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4108 # Points
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4109 # ref: https://r-charts.com/distribution/add-points-boxplot/
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4110 # NA values are not plotted
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4111 stripchart(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4112 blue_dots, # Data
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4113 method = "jitter", # Random noise
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4114 jitter = const_stripchart_jitter,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4115 pch = 19, # Pch symbols
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4116 cex = const_stripchart_cex, # Size of symbols reduced
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4117 col = "lightblue", # Color of the symbol
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4118 vertical = TRUE, # Vertical mode
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4119 add = TRUE # Add it over
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4120 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4121 stripchart(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4122 red_dots, # Data
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4123 method = "jitter", # Random noise
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4124 jitter = const_stripchart_jitter,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4125 pch = 19, # Pch symbols
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4126 cex = const_stripchart_cex, # Size of symbols reduced
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4127 col = "red", # Color of the symbol
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4128 vertical = TRUE, # Vertical mode
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4129 add = TRUE # Add it over
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4130 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4131
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4132 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4133 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4134 ```
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4135
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4136 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4137 if (sum(is.na(quant_data)) > 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4138 # show measured values in blue on left half-violin plot
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4139 cat("\\leavevmode\n\\quad\n\n\\quad\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4140 old_par <- par(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4141 mai = par("mai") + c(g_ppep_distrib_ctl$mai_bottom, 0, 0, 0),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4142 cex.axis = g_ppep_distrib_ctl$axis,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4143 cex.lab = 1.2
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4144 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4145 tryCatch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4146 {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4147 vioplot::vioplot(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4148 x = lapply(blue_dots, function(x) x[!is.na(x)]),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4149 col = "lightblue1",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4150 side = "left",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4151 plotCentre = "line",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4152 ylim = ylim_save,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4153 main = "Distributions of observed and imputed data",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4154 sub = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4155 las = 2,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4156 xlab = NULL,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4157 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4158 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4159 title(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4160 sub = "Light blue = observed data; Pink = imputed data",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4161 cex.sub = 1.0,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4162 line = g_ppep_distrib_ctl$xlab_line + 1
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4163 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4164 title(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4165 xlab = "Sample",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4166 line = g_ppep_distrib_ctl$xlab_line
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4167 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4168 red_violins <- lapply(red_dots, function(x) x[!is.na(x)])
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4169 cols_to_delete <- c()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4170 for (ix in seq_len(length(red_violins))) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4171 if (length(red_violins[[ix]]) < 1) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4172 cols_to_delete <- c(cols_to_delete, ix)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4173 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4174 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4175 # destroy any unimputable columns
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4176 if (!is.null(cols_to_delete)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4177 red_violins <- red_violins[-cols_to_delete]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4178 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4179 # plot imputed values in red on right half-violin plot
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4180 vioplot::vioplot(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4181 x = red_violins,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4182 col = "lightpink1",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4183 side = "right",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4184 plotCentre = "line",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4185 add = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4186 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4187
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4188 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4189 finally = par(old_par)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4190 )
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4191
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4192 # density plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4193 cat("\\leavevmode\n\n\n\n\n\n\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4194 if (can_plot_before_after_imp) {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4195 ylim <- c(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4196 0,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4197 max(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4198 if (is.list(d_combined)) d_combined$y else d_combined,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4199 if (is.list(d_original)) d_original$y else d_original,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4200 if (is.list(d_imputed)) d_imputed$y else d_imputed,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4201 na.rm = TRUE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4202 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4203 )
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4204 plot(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4205 d_combined,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4206 ylim = ylim,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4207 sub =
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4208 paste(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4209 "Blue = data before imputation; Red = imputed data;",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4210 "Black = combined"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4211 ),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4212 main = "Density of peptide intensity before and after imputation",
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4213 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"),
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4214 ylab = "Probability density"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4215 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4216 lines(d_original, col = "blue")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4217 lines(d_imputed, col = "red")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4218 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4219 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4220 "There are too few points to plot the density of peptide intensity",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4221 "before and after imputation."
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4222 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
4223 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
4224 cat("\\leavevmode\\newpage\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
4225 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
4226 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
4227
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4228 # Quantile Normalization
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
4229
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
4230 The excellent `normalize.quantiles` function from
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
4231 *[the `preprocessCore` Bioconductor package](http://bioconductor.org/packages/release/bioc/html/preprocessCore.html)*
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
4232 performs "quantile normalization" as described Bolstad *et al.* (2003),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
4233 DOI *[10.1093/bioinformatics/19.2.185](https://doi.org/10.1093%2Fbioinformatics%2F19.2.185)*
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4234 and its supplementary material [http://bmbolstad.com/misc/normalize/normalize.html](http://bmbolstad.com/misc/normalize/normalize.html),
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
4235 i.e., it assumes that the goal is to detect
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
4236 subtle differences among grossly similar samples (having similar distributions)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4237 by equalizing intra-quantile quantitations^[Unfortunately,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4238 one software library upon which `preprocessCore` depends
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
4239 *[suffers from a concurrency defect](https://support.bioconductor.org/p/122925/#9135989)*
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4240 that requires that a specific, non-concurrent version of the library (`openblas` version $0.3.3$) be
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
4241 installed. The installation command equivalent to what was used to install the library to produce the results presented here is:
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4242 \linebreak
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4243 ` conda install bioconductor-preprocesscore openblas=0.3.3`].
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
4244
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
4245
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
4246 <!--
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4247 # Apply quantile normalization using preprocessCore::normalize.quantiles
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4248 # ---
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4249 # tool repository: http://bioconductor.org/packages/release/bioc/html/preprocessCore.html
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4250 # except this: https://support.bioconductor.org/p/122925/#9135989
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4251 # says to install it like this:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4252 # ```
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4253 # BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE, lib=.libPaths()[1])
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diff changeset
4254 # ```
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4255 # conda installation (necessary because of a bug in recent openblas):
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4256 # conda install bioconductor-preprocesscore openblas=0.3.3
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diff changeset
4257 # ...
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diff changeset
4258 # ---
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4259 # normalize.quantiles {preprocessCore} -- Quantile Normalization
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4260 #
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4261 # Description:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4262 # Using a normalization based upon quantiles, this function normalizes a
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4263 # matrix of probe level intensities.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4264 #
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4265 # THIS FUNCTIONS WILL HANDLE MISSING DATA (ie NA values), based on the
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4266 # assumption that the data is missing at random.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4267 #
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4268 # Usage:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4269 # normalize.quantiles(x, copy = TRUE, keep.names = FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4270 #
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4271 # Arguments:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4272 #
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4273 # - x: A matrix of intensities where each column corresponds to a chip and each row is a probe.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4274 #
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4275 # - copy: Make a copy of matrix before normalizing. Usually safer to work with a copy,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4276 # but in certain situations not making a copy of the matrix, but instead normalizing
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4277 # it in place will be more memory friendly.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4278 #
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4279 # - keep.names: Boolean option to preserve matrix row and column names in output.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4280 #
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diff changeset
4281 # Details:
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diff changeset
4282 # This method is based upon the concept of a quantile-quantile plot extended to n dimensions.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4283 # No special allowances are made for outliers. If you make use of quantile normalization
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4284 # please cite Bolstad et al, Bioinformatics (2003).
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diff changeset
4285 #
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diff changeset
4286 # This functions will handle missing data (ie NA values), based on
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4287 # the assumption that the data is missing at random.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4288 #
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diff changeset
4289 # Note that the current implementation optimizes for better memory usage
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
4290 # at the cost of some additional run-time.
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diff changeset
4291 #
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diff changeset
4292 # Value: A normalized matrix.
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diff changeset
4293 #
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diff changeset
4294 # Author: Ben Bolstad, bmbolstad.com
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diff changeset
4295 #
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diff changeset
4296 # References
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4297 #
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diff changeset
4298 # - Bolstad, B (2001) Probe Level Quantile Normalization of High Density Oligonucleotide
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diff changeset
4299 # Array Data. Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf
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diff changeset
4300 #
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diff changeset
4301 # - Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) A Comparison of
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4302 # Normalization Methods for High Density Oligonucleotide Array Data Based on Bias
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4303 # and Variance. Bioinformatics 19(2), pp 185-193. DOI 10.1093/bioinformatics/19.2.185
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4304 # http://bmbolstad.com/misc/normalize/normalize.html
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4305 # ...
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4306 -->
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4307 ```{r echo = FALSE, results = 'asis'}
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4308
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4309 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp)), "\n")
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4310 if (nrow(quant_data_imp) > 0) {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4311 quant_data_imp_qn <- preprocessCore::normalize.quantiles(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4312 as.matrix(quant_data_imp), keep.names = TRUE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4313 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4314 } else {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4315 quant_data_imp_qn <- as.matrix(quant_data_imp)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4316 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4317
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4318 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn)), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4319
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4320 quant_data_imp_qn <- as.data.frame(quant_data_imp_qn)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4321 write_debug_file(quant_data_imp_qn)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4322
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4323 quant_data_imp_qn_log <- log10(quant_data_imp_qn)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4324 write_debug_file(quant_data_imp_qn_log)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4325
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4326 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn_log)), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4327 if (print_nb_messages) nbe(see_variable(ncol(quant_data_imp_qn_log)), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4328
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4329 quant_data_imp_qn_ls <- t(scale(t(log10(quant_data_imp_qn))))
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4330
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4331 sel <- row_apply(quant_data_imp_qn_ls, any_nan)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4332 quant_data_imp_qn_ls2 <- quant_data_imp_qn_ls
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4333
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4334 quant_data_imp_qn_ls2 <- quant_data_imp_qn_ls2[which(sel), ]
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4335 quant_data_imp_qn_ls2 <- as.data.frame(quant_data_imp_qn_ls2)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4336
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4337 quant_data_imp_qn_ls <- as.data.frame(quant_data_imp_qn_ls)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4338
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4339 write_debug_file(quant_data_imp_qn_ls)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4340 write_debug_file(quant_data_imp_qn_ls2)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4341
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4342 # Create data.frame used by ANOVA analysis
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4343 data_table_imp_qn_lt <- cbind(full_data[1:9], quant_data_imp_qn_log)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4344 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4345
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4346 ## Are normalized, imputed, log-transformed sample distributions similar?
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4347
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4348 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'}
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4349
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4350 # Save unimputed quant_data_log for plotting below
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4351 unimputed_quant_data_log <- quant_data_log
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4352
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4353 # log10 transform (after preparing for zero values,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4354 # which should never happen...)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4355 quant_data_imp_qn[quant_data_imp_qn == 0] <- .000000001
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4356 quant_data_log <- log10(quant_data_imp_qn)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4357
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4358 how_many_peptides <- nrow(quant_data_log)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4359
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4360 if ((how_many_peptides) > 0) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4361 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4362 sprintf(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4363 "Intensities for %d peptides:\n\n\n",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4364 how_many_peptides
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4365 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4366 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4367 cat("\n\n\n")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4368
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4369
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4370 # data visualization
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4371 if (TRUE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4372
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4373 my_ppep_distrib_bxp(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4374 x = quant_data_log
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4375 , sample_name_grow = sample_name_grow
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4376 , main = "Peptide intensities for each sample"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4377 , varwidth = boxplot_varwidth
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4378 , sub = NULL
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4379 , xlab = "Sample"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4380 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4381 , col = const_boxplot_fill
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4382 , notch = boxplot_notch
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4383 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4384
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4385 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4386
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4387 old_par <- par(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4388 mai = par("mai") + c(0.5, 0, 0, 0)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4389 , oma = par("oma") + c(0.5, 0, 0, 0)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4390 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4391 # ref: https://r-charts.com/distribution/add-points-boxplot/
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4392 # Vertical plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4393 colnames(quant_data_log) <- sample_name_matches
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4394 boxplot(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4395 quant_data_log
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
4396 , las = 2
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4397 , cex.axis = 0.9 * sample_name_grow
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4398 , col = const_boxplot_fill
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4399 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4400 , xlab = "Sample"
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4401 , notch = boxplot_notch
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4402 , varwidth = boxplot_varwidth
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4403 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4404 par(old_par)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4405 }
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4406 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4407 cat("There are no peptides to plot\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4408 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4409
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4410 cat("\n\n\n")
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4411
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4412 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4413
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4414 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4415 if (nrow(quant_data_log) > 1) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4416 quant_data_log_stack <- stack(quant_data_log)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4417 ggplot2::ggplot(quant_data_log_stack, ggplot2::aes(x = values)) +
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4418 ggplot2::xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) +
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4419 ggplot2::ylab("Probability density") +
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4420 ggplot2::geom_density(ggplot2::aes(group = ind, colour = ind), na.rm = TRUE)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4421 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4422 cat("No density plot because there are fewer than two peptides to plot.\n\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4423 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4424 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4425 ```{r echo = FALSE, results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4426 cat("\\leavevmode\\newpage\n")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4427 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4428
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4429 # ANOVA Analysis
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4430
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4431 ## Assignment of $p$-value and quality score
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4432
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4433 For each phosphopeptide, ANOVA analysis was performed to compute a $p$-value representing the evidence against the "null hypothesis" ($H_0$) that the intensity does not vary significantly among sample groups.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4434
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4435 However, because as more and more phosphopeptides are tested, there is increasd probability that, by random chance, a given peptide will have a $p$-value that appears to indicate significance. For this reason, the $p$-values were adjusted by applying the False Discovery Rate (FDR) correction from Benjamini and Hochberg (1995) [doi:10.1111/j.2517-6161.1995.tb02031.x](https:/doi.org/10.1111/j.2517-6161.1995.tb02031.x).
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4436
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4437 Furthermore, to give more weight to phosphopeptides having fewer missing values, an (arbitrarily defined) quality score was assigned to each, defined as:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4438
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4439 $$
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4440 \textit{quality}_j
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4441 = \frac{1 + o_{j}}{v_{j}(1 + o_{j}) + 0.005}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4442 $$
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4443
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4444 where:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4445
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4446 - $o_j$ is the minimum number of non-missing observations per sample group for substrate $j$ for all sample groups, and
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4447 - $v_j$ is the FDR-adjusted ANOVA $p$-value for substrate $j$.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4448
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4449
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4450 ```{r, echo = FALSE, results = 'asis'}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4451 cat("\\newpage\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4452
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4453 # Make new data frame containing only Phosphopeptides
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4454 # to connect preANOVA to ANOVA (connect_df)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4455 connect_df <- data.frame(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4456 data_table_imp_qn_lt$Phosphopeptide
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4457 , data_table_imp_qn_lt[, first_data_column]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4458 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4459 colnames(connect_df) <- c("Phosphopeptide", "Intensity")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4460 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4461
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4462 ```{r anova, echo = FALSE, fig.dim = c(10, 12), results = 'asis'}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4463 g_can_run_ksea <- FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4464 old_oma <- par("oma")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4465 if (count_of_treatment_levels < 2) {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4466 cat(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4467 "ERROR!!!! Cannot perform ANOVA analysis",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4468 "(see next page)\\newpage\n"
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4469 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4470 cat(
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4471 "ERROR: ANOVA analysis",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4472 "requires two or more factor levels!\n\n\n"
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4473 )
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4474
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4475 cat("\n\n\n\n\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4476 cat("Unparsed sample names are:\n\n\n",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4477 "\\begin{quote}\n",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4478 paste(names(quant_data_imp_qn_log), collapse = "\n\n\n"),
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4479 "\n\\end{quote}\n\n")
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4480
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4481 regex_sample_names <- latex_printable_control_seqs(regex_sample_names)
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4482
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4483 cat("\\leavevmode\n\n\n")
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4484 cat("Parsing rule for SampleNames is",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4485 "\n\n\n",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4486 "\\text{'",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4487 regex_sample_names,
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4488 "'}\n\n\n",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4489 sep = ""
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4490 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4491
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4492 cat("\nParsed sample names are:\n",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4493 "\\begin{quote}\n",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4494 paste(sample_name_matches, collapse = "\n\n\n"),
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4495 "\n\\end{quote}\n\n")
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4496
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4497 regex_sample_grouping <- latex_printable_control_seqs(regex_sample_grouping)
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4498
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4499 cat("\\leavevmode\n\n\n")
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4500 cat("Parsing rule for SampleGrouping is",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4501 "\n\n\n",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4502 "\\text{'",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4503 regex_sample_grouping,
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4504 "'}\n\n\n",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4505 sep = ""
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4506 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4507
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4508 cat("\n\n\n")
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4509 cat("Sample group assignments are:\n",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4510 "\\begin{quote}\n",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4511 paste(regmatches(sample_name_matches, rx_match), collapse = "\n\n\n"),
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4512 "\n\\end{quote}\n\n")
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
4513
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4514 } else {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4515
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4516 if (print_nb_messages) nbe("computing p_value_data_anova_ps\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4517 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn_log)), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4518 if (print_nb_messages) nbe(see_variable(ncol(quant_data_imp_qn_log)), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4519 if (print_nb_messages) nbe(see_variable(quant_data_imp_qn_log[, ".NE.7C"]), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4520 if (print_nb_messages) nbe(see_variable(quant_data_imp_qn_log), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4521 if (print_nb_messages) nbe(see_variable(anova_func), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4522 if (print_nb_messages) nbe(see_variable(smpl_trt), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4523 if (print_nb_messages) nbe(see_variable(one_way_all_categories), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4524 tryCatch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4525 {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4526 p_value_data_anova_ps <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4527 row_apply(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4528 quant_data_imp_qn_log,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4529 anova_func,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4530 grouping_factor = smpl_trt,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4531 one_way_f = one_way_all_categories
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4532 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4533 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4534 error = function(e) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4535 mesg <- paste("Could not compute ANOVA because", e$message)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4536 cat("\n\n", mesg, "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4537 param_df_noexit(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4538 sink(stderr())
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4539 cat("\n\n", mesg, "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4540 values <- paste(param_df$parameter, "=", param_df$value, collapse = "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4541 cat(values)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4542 sink()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4543 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4544 exit(code = 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4545 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4546 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4547 if (print_nb_messages) nbe(see_variable(p_value_data_anova_ps), "\n")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4548
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4549 p_value_data_anova_ps_fdr <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4550 p.adjust(p_value_data_anova_ps, method = "fdr")
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4551 my_ppep_v <- full_data[, 1]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4552 p_value_data <- list(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4553 phosphopeptide = my_ppep_v,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4554 raw_anova_p = p_value_data_anova_ps,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4555 fdr_adjusted_anova_p = p_value_data_anova_ps_fdr,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4556 missing_values = rowSums(is.na(quant_data)),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4557 min_group_obs_count = min_group_obs_count
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4558 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4559 p_value_data <- data.frame(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4560 phosphopeptide = my_ppep_v,
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
4561 raw_anova_p = p_value_data_anova_ps,
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4562 fdr_adjusted_anova_p = p_value_data_anova_ps_fdr,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4563 missing_values = rowSums(is.na(quant_data)),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4564 min_group_obs_count = min_group_obs_count
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4565 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4566 p_value_data$quality <- 1.0 / with(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4567 p_value_data,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4568 fdr_adjusted_anova_p + 0.005 / (1 + min_group_obs_count)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4569 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4570
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4571 p_value_data$ranking <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4572 with(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4573 p_value_data,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4574 switch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4575 g_intensity_hm_criteria,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4576 "quality" = order(-quality),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4577 "na_count" = order(missing_values, fdr_adjusted_anova_p),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4578 # the default is "p_value"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4579 order(fdr_adjusted_anova_p)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4580 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4581 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4582 p_value_data <- p_value_data[p_value_data$ranking, , drop = FALSE]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4583
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4584 write.table(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4585 p_value_data,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4586 file = "p_value_data.txt",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4587 sep = "\t",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4588 col.names = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4589 row.names = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4590 quote = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4591 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4592
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4593
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4594 # output ANOVA file to constructed filename,
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4595 # e.g. "Outputfile_pST_ANOVA_STEP5.txt"
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4596 # becomes "Outputfile_pST_ANOVA_STEP5_FDR0.05.txt"
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4597
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4598 # Re-output datasets to include p-values
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4599 metadata_plus_p <- cbind(full_data[1:9], p_value_data[, 2:ncol(p_value_data)])
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4600 write.table(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4601 cbind(metadata_plus_p, quant_data_imp),
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4602 file = imputed_data_filename,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4603 sep = "\t",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4604 col.names = TRUE,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4605 row.names = FALSE,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4606 quote = FALSE
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4607 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4608
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4609 write.table(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4610 cbind(metadata_plus_p, quant_data_imp_qn_log),
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4611 file = imp_qn_lt_data_filenm,
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4612 sep = "\t",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4613 col.names = TRUE,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4614 row.names = FALSE,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4615 quote = FALSE
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4616 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4617
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4618
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4619 first_page_suppress <- 1
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4620 number_of_peptides_found <- 0
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4621 cutoff <- val_fdr[1]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4622 for (cutoff in val_fdr) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4623 #loop through FDR cutoffs
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4624 if (number_of_peptides_found > g_intensity_hm_rows - 1) {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4625 cat("\\leavevmode\n\n\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4626 break
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4627 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4628
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4629 bool_1 <- (p_value_data$fdr_adjusted_anova_p < cutoff)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4630 bool_2 <- (p_value_data$min_group_obs_count >= g_intensity_min_per_class)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4631 g_can_run_ksea <- g_can_run_ksea || (sum(bool_2) > 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4632 bool_4 <- (p_value_data$quality >= params$minQuality)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4633 bool_3 <- as.logical(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4634 as.integer(bool_1) *
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4635 as.integer(bool_2) *
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4636 as.integer(bool_4)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4637 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4638 if (print_trace_messages) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4639 if (length(bool_1) > 30) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4640 cat_variable(bool_1, force_str = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4641 cat_variable(bool_2, force_str = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4642 cat_variable(bool_3, force_str = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4643 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4644 cat_variable(bool_1, suffix = "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4645 cat_variable(bool_2, suffix = "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4646 cat_variable(bool_3, suffix = "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4647 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4648 cat_variable(length(bool_3), digits = 0, suffix = "; ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4649 cat_variable(sum(bool_3), digits = 0, suffix = "\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4650 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4651
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4652 filtered_p <-
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4653 p_value_data[bool_3, , drop = FALSE]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4654 filtered_p <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4655 filtered_p[!is.na(filtered_p$phosphopeptide), , drop = FALSE]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4656
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4657 if (print_trace_messages)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4658 cat_variable(filtered_p, force_str = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4659
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4660 have_remaining_peptides <- sum(bool_3, na.rm = TRUE) > 0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4661 filter_result_string <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4662 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4663 "%s, %s of %0.0f peptides remained having both %s and %s.\n\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4664 "After filtering for ANOVA results",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4665 if (have_remaining_peptides)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4666 as.character(sum(bool_3, na.rm = TRUE))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4667 else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4668 "none",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4669 length(bool_3),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4670 sprintf("adjusted p-value < %s", as.character(signif(cutoff, 2))),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4671 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4672 "more than %0.0f observations in some groups",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4673 max(0, g_intensity_min_per_class - 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4674 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4675 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4676
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4677 filtered_data_filtered <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4678 quant_data_imp_qn_log[
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4679 rownames(filtered_p),
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4680 , drop = FALSE
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4681 ]
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4682 # order by p-value
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4683 filtered_data_filtered <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4684 filtered_data_filtered[
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4685 order(filtered_p$fdr_adjusted_anova_p),
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4686 , drop = FALSE
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4687 ]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4688
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4689 if (have_remaining_peptides && nrow(filtered_p) > 0 && nrow(filtered_data_filtered) > 0) {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4690 if (first_page_suppress == 1) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4691 first_page_suppress <- 0
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4692 } else {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4693 cat("\\newpage\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4694 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4695 latex_samepage({
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4696 cat(filter_result_string)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4697 if (nrow(filtered_data_filtered) > 1) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4698 cat(subsection_header(sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4699 "Intensity distributions for %d phosphopeptides\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4700 nrow(filtered_data_filtered)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4701 )))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4702 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4703 cat(subsection_header(sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4704 "Intensity distribution for one phosphopeptide (%s)\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4705 rownames(filtered_data_filtered)[1]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4706 )))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4707 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4708 }) # end latex_samepage
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4709
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4710 old_par <- par(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4711 mai = (par("mai") + c(0.7, 0, 0, 0)) * c(1, 1, 0.3, 1),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4712 oma = old_oma * c(1, 1, 0.3, 1),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4713 cex.main = 0.9,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4714 cex.axis = 0.7,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4715 fin = c(9, 7.25)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4716 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4717 # Vertical plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4718 colnames(filtered_data_filtered) <- sample_name_matches
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4719 tryCatch(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4720 boxplot(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4721 filtered_data_filtered,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4722 main = "Imputed, normalized intensities", # no line plot
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
4723 las = 2,
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4724 cex.axis = 0.9 * sample_name_grow,
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4725 col = const_boxplot_fill,
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4726 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)"),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4727 notch = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4728 varwidth = boxplot_varwidth
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4729 ),
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4730 error = function(e) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4731 print(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4732 cat_margins()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4733 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4734
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4735 )
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4736 par(old_par)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4737 } else {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4738 cat(sprintf(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4739 "%s < %0.2f\n\n\n\n\n",
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
4740 "No peptides were found to have cutoff adjusted p-value",
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4741 cutoff
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4742 ))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4743 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4744
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4745 if (have_remaining_peptides && nrow(filtered_data_filtered) > 0) {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4746 # Add Phosphopeptide column to anova_filtered table
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4747 # The assumption here is that the first intensity is unique;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4748 # this is a hokey assumption but almost definitely will
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4749 # be true in the real world unless there is a computation
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4750 # error upstream.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4751 anova_filtered_merge <- base::merge(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4752 x = connect_df,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4753 y = filtered_data_filtered,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4754 by.x = "Intensity",
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4755 by.y = 1
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4756 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4757 anova_filtered_merge_order <- rownames(filtered_p)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4758
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4759 anova_filtered <- data.frame(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4760 ppep = anova_filtered_merge$Phosphopeptide,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4761 intense = anova_filtered_merge$Intensity,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4762 data = anova_filtered_merge[, 2:number_of_samples + 1]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4763 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4764 colnames(anova_filtered) <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4765 c("Phosphopeptide", colnames(filtered_data_filtered))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4766
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4767 # Merge qualitative columns into the ANOVA data
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4768 output_table <- data.frame(anova_filtered$Phosphopeptide)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4769 output_table <- base::merge(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4770 x = output_table,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4771 y = data_table_imp_qn_lt,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4772 by.x = "anova_filtered.Phosphopeptide",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4773 by.y = "Phosphopeptide"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4774 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4775
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4776 # Produce heatmap to visualize significance and the effect of imputation
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4777
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4778 cat_hm_heading <- function(m, cutoff) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4779 if (nrow(m) > g_intensity_hm_rows) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4780 cat("\\clearpage\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4781 cat(subsection_header(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4782 paste(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4783 sprintf("Heatmap for the %d most-significant peptides",
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4784 g_intensity_hm_rows),
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4785 sprintf("whose adjusted p-value < %0.2f\n", cutoff)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4786 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4787 ))
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4788 } else {
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
4789 if (nrow(m) == 0) {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4790 return(FALSE)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4791 } else {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4792 cat(subsection_header(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4793 paste(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4794 sprintf("Heatmap for %d usable peptide genes whose", nrow(m)),
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4795 sprintf("adjusted p-value < %0.2f\n", cutoff)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4796 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4797 ))
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4798 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4799 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4800 cat("\n\n\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4801 cat("\n\n\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4802 return(TRUE)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4803 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4804
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4805 # construct matrix with appropriate rownames
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4806 m <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4807 as.matrix(unimputed_quant_data_log[anova_filtered_merge_order, ])
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4808 nrow_m <- nrow(m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4809 ncol_m <- ncol(m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4810 if (nrow_m > 0) {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4811 rownames_m <- rownames(m)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4812 q <- data.frame(pepname = rownames_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4813 g <- sqldf("
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4814 SELECT q.pepname, substr(met.Gene_Name, 1, 30) AS gene_name
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4815 FROM q, metadata_plus_p AS met
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4816 WHERE q.pepname = met.Phosphopeptide
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4817 ORDER BY q.rowid
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4818 ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4819 tmp <- sapply(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4820 X = seq_len(nrow(g)),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4821 FUN = function(i) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4822 pre <- strsplit(g$gene_name[i], "; ")[[1]]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4823 rslt <- paste(unique(pre), sep = "; ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4824 return(rslt)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4825 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4826 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4827 tmp <- unlist(tmp)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4828 tmp <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4829 make.names(tmp, unique = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4830 tmp <- sub(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4831 "No_Gene_Name",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4832 "not_found",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4833 tmp,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4834 fixed = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4835 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4836 ten_trunc_names <- trunc_ppep(rownames_m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4837 tmp <- sapply(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4838 X = seq_len(nrow_m),
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4839 FUN = function(i) {
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4840 sprintf(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4841 "(%s) %s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4842 tmp[i],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4843 ten_trunc_names[i]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4844 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4845 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4846 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4847 rownames(m) <- tmp
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4848 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4849 # draw the heading and heatmap
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4850 if (nrow_m > 0) {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4851 number_of_peptides_found <-
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4852 ppep_heatmap(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4853 m = m,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4854 cutoff = cutoff,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4855 hm_heading_function = cat_hm_heading,
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
4856 hm_main_title =
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
4857 "log(intensities), row-scaled, unimputed, unnormalized",
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4858 suppress_row_dendrogram = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4859 master_cex = 0.35,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4860 sepcolor = "black",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4861 colsep = sample_colsep
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
4862 )
25
f9cd87ac8006 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c58b9b301977f191acd40a22b630177c381317ca
eschen42
parents: 24
diff changeset
4863 if (number_of_peptides_found > 1) {
f9cd87ac8006 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c58b9b301977f191acd40a22b630177c381317ca
eschen42
parents: 24
diff changeset
4864 cat("\\leavevmode\n")
f9cd87ac8006 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c58b9b301977f191acd40a22b630177c381317ca
eschen42
parents: 24
diff changeset
4865 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
4866 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4867 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4868 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4869 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4870 cat(filter_result_string)
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
4871 cat("\\leavevmode\n")
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4872
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4873 if (!g_can_run_ksea) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4874 errmsg <- paste("Cannot proceed with KSEA analysis",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4875 "because too many values are missing.")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4876 if (FALSE) cat0(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4877 errmsg,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4878 "\\stepcounter{offset}\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4879 "\\stepcounter{offset}\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4880 "\\stepcounter{offset}\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4881 " in ",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4882 table_href(),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4883 ".\n\n"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4884 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4885 if (FALSE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4886 if (print_nb_messages) nbe(see_variable(p_value_data))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4887 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4888 if (print_nb_messages) nbe(see_variable(p_value_data))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4889
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4890 display_p_value_data <- p_value_data
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4891 display_p_value_data$raw_anova_p <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4892 sprintf("%0.3g", display_p_value_data$raw_anova_p)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4893 display_p_value_data$fdr_adjusted_anova_p <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4894 sprintf("%0.3g", display_p_value_data$fdr_adjusted_anova_p)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4895 display_p_value_data$quality <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4896 sprintf("%0.3g", display_p_value_data$quality)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4897
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4898 headers_1st_line <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
4899 c("", "Raw ANOVA", "FDR-adj.", "Missing", "Min. #", "", "")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4900 headers_2nd_line <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
4901 c("Phosphopeptide", "p-value", "p-value", "values", "group-obs", "Quality", "Ranking")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4902 data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4903 x = display_p_value_data,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
4904 tabstops = c(2.75, 0.80, 0.80, 0.5, 0.6, 0.60),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4905 use_subsubsection_header = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4906 headings = c(headers_1st_line, headers_2nd_line),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4907 caption = "ANOVA results"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4908
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4909 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4910 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4911 data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4912 x = save_sample_treatment_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4913 tabstops = c(1.25, 1.25),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4914 caption = "Sample classes",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4915 use_subsubsection_header = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4916 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4917 param_df_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4918 knitr::knit_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4919 return(invisible(-1))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4920 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4921
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
4922 ```
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4923
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
4924 ```{r sqlite, echo = FALSE, fig.dim = c(9, 10), results = 'asis'}
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4925
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4926 if (g_can_run_ksea && count_of_treatment_levels > 1) {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4927 # Prepare two-way contrasts with adjusted p-values
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4928 # Strategy:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4929 # - use imputed, log-transformed data:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4930 # - remember this when computing log2(fold-change)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4931 # - each contrast is between a combination of trt levels
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4932 # - for each contrast, compute samples that are members
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4933 # - compute one-way test:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4934 # - use `oneway.test` (Welch test) if numbers of samples
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4935 # are not equivalent between trt levels
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4936 # - otherwise, aov is fine but offers no advantage
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4937 # - adjust p-value, assuming that
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4938 # (# of pppeps)*(# of contrasts) tests were performed
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4939
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4940 # Each contrast is between a combination of trt levels
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4941 m2 <- combn(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4942 x = seq_len(length(levels(smpl_trt))),
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4943 m = 2,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4944 simplify = TRUE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4945 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4946 contrast_count <- ncol(m2)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4947
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4948 # For each contrast, compute samples that are members
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4949 # - local function to construct a data.frame for each contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4950 # - the contrast in the first "column"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4951 f_m2 <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4952 function(cntrst, lvl1, lvl2) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4953 return(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4954 data.frame(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4955 contrast = cntrst,
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4956 level = smpl_trt[
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4957 smpl_trt %in%
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4958 levels(smpl_trt)[c(lvl1, lvl2)]
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4959 ],
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4960 label = sample_name_matches[
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4961 smpl_trt %in%
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
4962 levels(smpl_trt)[c(lvl1, lvl2)]
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4963 ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4964 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4965 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4966 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4967 # - compute a df for each contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4968 sample_level_dfs <- lapply(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4969 X = 1:contrast_count,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4970 FUN = function(i) f_m2(i, m2[1, i], m2[2, i])
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4971 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4972 # - compute a single df for all contrasts
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4973 combined_contrast_df <- Reduce(f = rbind, x = sample_level_dfs)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4974
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4975 # - dispose objects to free resources
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4976 rm(sample_level_dfs)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4977
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4978 # - write the df to a DB for later join-per-contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4979 db <- RSQLite::dbConnect(RSQLite::SQLite(), ksea_app_prep_db)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4980
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4981 RSQLite::dbWriteTable(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4982 conn = db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4983 name = "contrast",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4984 value = combined_contrast_df,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4985 overwrite = TRUE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4986 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4987
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4988 # Create UK for insert
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4989 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4990 CREATE UNIQUE INDEX IF NOT EXISTS contrast__uk__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4991 ON contrast(contrast, label);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4992 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4993 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4994 # Create indexes for join
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4995 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4996 -- index for join in contrast_ppep_smpl_qnlt on a.label < b.label
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4997 CREATE INDEX IF NOT EXISTS contrast__label__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4998 ON contrast(label);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
4999 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5000 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5001 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5002 -- index for joining two contrast_lvl_ppep_avg_quant on contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5003 CREATE INDEX IF NOT EXISTS contrast__contrast__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5004 ON contrast(contrast);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5005 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5006 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5007 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5008 -- index for joining two contrast_lvl_ppep_avg_quant on phophospep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5009 CREATE INDEX IF NOT EXISTS contrast__level__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5010 ON contrast(level);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5011 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5012 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5013 # - dispose objects to free resources
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5014 rm(combined_contrast_df)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5015
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5016 # Use imputed, log-transformed data
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5017 # - remember that this was donoe when computing log2(fold-change)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5018 # - melt data matrix for use in later join-per-contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5019 casted <- cbind(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5020 data.frame(vrbl = rownames(quant_data_imp_qn_log)),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5021 quant_data_imp_qn_log
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5022 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5023 quant_data_imp_qn_log_melted <- reshape2::melt(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5024 casted,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5025 id.vars = "vrbl"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5026 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5027 colnames(quant_data_imp_qn_log_melted) <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5028 c("phosphopep", "sample", "quant")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5029 # - dispose objects to free resources
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5030 rm(casted)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5031
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5032 # - write the df to a DB for use in later join-per-contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5033 RSQLite::dbWriteTable(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5034 conn = db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5035 name = "ppep_smpl_qnlt",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5036 value = quant_data_imp_qn_log_melted,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5037 overwrite = TRUE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5038 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5039 # Create UK for insert
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5040 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5041 CREATE UNIQUE INDEX IF NOT EXISTS ppep_smpl_qnlt__uk__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5042 ON ppep_smpl_qnlt(phosphopep, sample);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5043 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5044 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5045 # Create index for join
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5046 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5047 -- index for join in contrast_ppep_smpl_qnlt
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5048 CREATE INDEX IF NOT EXISTS ppep_smpl_qnlt__sample__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5049 ON ppep_smpl_qnlt(sample);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5050 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5051 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5052 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5053 -- index for joining two contrast_lvl_ppep_avg_quant on phopho.pep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5054 CREATE INDEX IF NOT EXISTS ppep_smpl_qnlt__phosphopep__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5055 ON ppep_smpl_qnlt(phosphopep);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5056 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5057 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5058 # - dispose objects to free resources
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5059 rm(quant_data_imp_qn_log_melted)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5060
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5061 # - drop views if exist
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5062 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5063 -- drop view dependent on contrast_lvl_ppep_avg_quant
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5064 DROP VIEW IF EXISTS v_contrast_log2_fc;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5065 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5066 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5067 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5068 -- drop table dependent on contrast_ppep_smpl_qnlt
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5069 DROP TABLE IF EXISTS contrast_lvl_ppep_avg_quant;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5070 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5071 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5072 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5073 DROP TABLE IF EXISTS contrast_lvl_lvl_metadata;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5074 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5075 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5076 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5077 DROP VIEW IF EXISTS v_contrast_lvl_metadata;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5078 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5079 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5080 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5081 -- drop view dependent on contrast_ppep_smpl_qnlt
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5082 DROP VIEW IF EXISTS v_contrast_lvl_ppep_avg_quant;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5083 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5084 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5085 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5086 DROP VIEW IF EXISTS v_contrast_lvl_lvl;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5087 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5088 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5089 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5090 -- drop view upon which other views depend
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5091 DROP VIEW IF EXISTS contrast_ppep_smpl_qnlt;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5092 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5093 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5094 # - create view
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5095 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5096 -- view contrast_ppep_smpl_qnlt is used for each phopshopep to
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5097 -- compute p-value for test of trt effect for two trt levels
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5098 CREATE VIEW contrast_ppep_smpl_qnlt
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5099 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5100 SELECT contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5101 level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5102 phosphopep,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5103 sample,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5104 quant
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5105 FROM contrast AS c,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5106 ppep_smpl_qnlt AS q
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5107 WHERE q.sample = c.label
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5108 ORDER BY contrast, level, phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5109 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5110 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5111 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5112 # - create simplification views
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5113 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5114 CREATE VIEW v_contrast_lvl_metadata
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5115 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5116 SELECT contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5117 level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5118 group_concat(label, ';') AS samples
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5119 FROM contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5120 GROUP BY contrast, level
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5121 /* view v_contrast_lvl_metadata is used
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5122 to simplify creation of table contrast_lvl_lvl_metadata */
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5123 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5124 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5125 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5126 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5127 CREATE VIEW v_contrast_lvl_ppep_avg_quant
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5128 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5129 SELECT contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5130 level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5131 phosphopep,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5132 avg(quant) AS avg_quant
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5133 FROM contrast_ppep_smpl_qnlt
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5134 GROUP BY contrast, level, phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5135 /* view v_contrast_lvl_ppep_avg_quant is used
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5136 to simplify view v_contrast_log2_fc */
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5137 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5138 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5139 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5140
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5141 # - create contrast-metadata table
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5142 if (print_nb_messages) nbe("CREATE TABLE contrast_lvl_lvl_metadata")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5143 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5144 CREATE TABLE contrast_lvl_lvl_metadata
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5145 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5146 SELECT DISTINCT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5147 a.contrast AS ab_contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5148 a.level AS a_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5149 b.level AS b_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5150 a.samples AS a_samples,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5151 b.samples AS b_samples,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5152 'log2(level_'||a.level||'/level_'||b.level||')'
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5153 AS fc_description
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5154 FROM v_contrast_lvl_metadata AS a,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5155 v_contrast_lvl_metadata AS b
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5156 WHERE a.contrast = b.contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5157 AND a.level > b.level
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5158 /* view v_contrast_lvl_lvl is used
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5159 to simplify view v_contrast_log2_fc */
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5160 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5161 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5162 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5163 # - create pseudo-materialized view table
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5164 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5165 CREATE VIEW v_contrast_lvl_lvl
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5166 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5167 SELECT DISTINCT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5168 a.contrast AS ab_contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5169 a.level AS a_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5170 b.level AS b_level
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5171 FROM contrast AS a,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5172 contrast AS b
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5173 WHERE a.contrast = b.contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5174 AND a.level > b.level
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5175 /* view v_contrast_lvl_lvl is used
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5176 to simplify view v_contrast_log2_fc */
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5177 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5178 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5179 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5180
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5181 # - create view to compute log2(fold-change)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5182 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5183 CREATE VIEW v_contrast_log2_fc
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5184 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5185 SELECT ab.ab_contrast AS contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5186 m.a_level AS a_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5187 c.avg_quant AS a_quant,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5188 m.a_samples AS a_samples,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5189 ab.b_level AS b_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5190 d.avg_quant AS b_quant,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5191 m.b_samples AS b_samples,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5192 m.fc_description AS fc_description,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5193 3.32193 * ( d.avg_quant - c.avg_quant) AS log2_fc,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5194 d.phosphopep AS phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5195 FROM contrast_lvl_lvl_metadata AS m,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5196 v_contrast_lvl_ppep_avg_quant AS d,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5197 v_contrast_lvl_lvl AS ab
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5198 INNER JOIN v_contrast_lvl_ppep_avg_quant AS c
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5199 ON c.contrast = ab.ab_contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5200 AND c.level = ab.a_level
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5201 WHERE d.contrast = ab.ab_contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5202 AND m.ab_contrast = ab.ab_contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5203 AND d.level = ab.b_level
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5204 AND d.phosphopep = c.phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5205 /* view to compute log2(fold-change) */
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5206 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5207 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5208 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5209
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5210 # For each contrast, compute samples that are members
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5211 # compute one-way test:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5212 # - use `oneway.test` (Welch test) if numbers of samples
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5213 # are not equivalent between trt levels
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5214 # - otherwise, aov is fine but offers no advantage
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5215 for (contrast in contrast_count:2) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5216 invisible(contrast)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5217 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5218 for (contrast in 1:contrast_count) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5219 contrast_df <- sqldf::sqldf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5220 x = paste0("
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5221 SELECT level, phosphopep, sample, quant
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5222 FROM contrast_ppep_smpl_qnlt
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5223 WHERE contrast = ", contrast, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5224 ORDER BY phosphopep, level, sample
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5225 "),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5226 connection = db
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5227 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5228 contrast_cast <- reshape2::dcast(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5229 data = contrast_df,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5230 formula = phosphopep ~ sample,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5231 value.var = "quant"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5232 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5233 contrast_cast_ncol <- ncol(contrast_cast)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5234 contrast_cast_data <- contrast_cast[, 2:contrast_cast_ncol]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5235 contrast_cast_samples <- colnames(contrast_cast_data)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5236
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5237 # - order grouping_factor by order of sample columns of contrast_cast_data
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5238 grouping_factor <- sqldf::sqldf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5239 x = paste0("
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5240 SELECT sample, level
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5241 FROM contrast_ppep_smpl_qnlt
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5242 WHERE contrast = ", contrast, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5243 ORDER BY phosphopep, level, sample
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5244 LIMIT ", contrast_cast_ncol - 1
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5245 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5246 connection = db
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5247 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5248 rownames(grouping_factor) <- grouping_factor$sample
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5249 grouping_factor <- grouping_factor[, "level", drop = FALSE]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5250
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5251 # - run the two-level (one-way) test
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5252 p_value_data_contrast_ps <-
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5253 row_apply(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5254 x = contrast_cast_data,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5255 fun = anova_func,
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5256 grouping_factor =
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
5257 as.factor(grouping_factor$level), # anova_func arg2
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5258 one_way_f = one_way_two_categories, # anova_func arg3
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5259 simplify = TRUE # TRUE is the default for simplify
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5260 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5261 contrast_data_adj_p_values <- p.adjust(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5262 p = p_value_data_contrast_ps,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5263 method = "fdr",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5264 n = length(p_value_data_contrast_ps) # this is the default, length(p)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5265 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5266 # - compute the fold-change
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5267 contrast_p_df <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5268 data.frame(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5269 contrast = contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5270 phosphopep = contrast_cast$phosphopep,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5271 p_value_raw = p_value_data_contrast_ps,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5272 p_value_adj = contrast_data_adj_p_values
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5273 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5274 db_write_table_overwrite <- (contrast < 2)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5275 db_write_table_append <- !db_write_table_overwrite
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5276 RSQLite::dbWriteTable(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5277 conn = db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5278 name = "contrast_ppep_p_val",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5279 value = contrast_p_df,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5280 append = db_write_table_append
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5281 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5282 # Create UK for insert
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5283 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5284 CREATE UNIQUE INDEX IF NOT EXISTS contrast_ppep_p_val__uk__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5285 ON contrast_ppep_p_val(phosphopep, contrast);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5286 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5287 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5288 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5289 # Perhaps this could be done more elegantly using unique keys
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5290 # or creating the tables before saving data to them, but this
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5291 # is fast and, if the database exists on disk rather than in
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5292 # memory, it doesn't stress memory.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5293 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5294 CREATE TEMP table contrast_log2_fc
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5295 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5296 SELECT *
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5297 FROM v_contrast_log2_fc
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5298 ORDER BY contrast, phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5299 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5300 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5301 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5302 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5303 CREATE TEMP table ppep_p_val
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5304 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5305 SELECT p_value_raw,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5306 p_value_adj,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5307 contrast AS p_val_contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5308 phosphopep AS p_val_ppep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5309 FROM contrast_ppep_p_val
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5310 ORDER BY contrast, phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5311 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5312 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5313 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5314 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5315 DROP TABLE IF EXISTS contrast_log2_fc_p_val
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5316 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5317 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5318 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5319 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5320 CREATE TABLE contrast_log2_fc_p_val
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5321 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5322 SELECT a.*,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5323 b.p_value_raw,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5324 b.p_value_adj,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5325 b.p_val_contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5326 b.p_val_ppep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5327 FROM contrast_log2_fc a, ppep_p_val b
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5328 WHERE a.rowid = b.rowid
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5329 AND a.phosphopep = b.p_val_ppep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5330 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5331 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5332 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5333 # Create UK
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5334 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5335 CREATE UNIQUE INDEX IF NOT EXISTS contrast_log2_fc_p_val__uk__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5336 ON contrast_log2_fc_p_val(phosphopep, contrast);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5337 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5338 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5339 # Create indices for future queries
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5340 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5341 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__contrast__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5342 ON contrast_log2_fc_p_val(contrast);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5343 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5344 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5345 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5346 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__phosphopep__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5347 ON contrast_log2_fc_p_val(phosphopep);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5348 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5349 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5350 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5351 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__p_value_raw__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5352 ON contrast_log2_fc_p_val(p_value_raw);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5353 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5354 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5355 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5356 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__p_value_adj__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5357 ON contrast_log2_fc_p_val(p_value_adj);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5358 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5359 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5360 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5361 DROP VIEW IF EXISTS v_contrast_log2_fc_p_val
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5362 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5363 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5364 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5365 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5366 CREATE VIEW v_contrast_log2_fc_p_val
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5367 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5368 SELECT contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5369 a_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5370 a_samples,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5371 b_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5372 b_samples,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5373 a_quant,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5374 b_quant,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5375 fc_description,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5376 log2_fc,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5377 p_value_raw,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5378 p_value_adj,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5379 phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5380 FROM contrast_log2_fc_p_val
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5381 ORDER BY contrast, phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5382 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5383 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5384 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5385 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5386 DROP TABLE IF EXISTS kseaapp_metadata
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5387 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5388 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5389 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5390 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5391 CREATE TABLE kseaapp_metadata
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5392 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5393 WITH extended(deppep, ppep, gene_name, uniprot_id, phosphoresidue) AS (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5394 SELECT DISTINCT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5395 deppep.seq,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5396 ppep.seq,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5397 GeneName||';',
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5398 UniProtID||';',
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5399 PhosphoResidue||';'
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5400 FROM
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5401 ppep, deppep, mrgfltr_metadata
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5402 WHERE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5403 mrgfltr_metadata.ppep_id = ppep.id
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5404 AND
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5405 ppep.deppep_id = deppep.id
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5406 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5407 SELECT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5408 ppep AS `ppep`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5409 SUBSTR(uniprot_id, 1, INSTR(uniprot_id,';') - 1 ) AS `Protein`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5410 SUBSTR(gene_name, 1, INSTR(gene_name,';') - 1 ) AS `Gene`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5411 deppep AS `Peptide`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5412 REPLACE(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5413 REPLACE(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5414 SUBSTR(phosphoresidue, 1, INSTR(phosphoresidue,';') - 1 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5415 'p',
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5416 ''
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5417 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5418 ', ',
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5419 ';'
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5420 ) AS `Residue.Both`
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5421 FROM extended
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5422 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5423 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5424 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5425 # Create indexes for join
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5426 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5427 CREATE INDEX IF NOT EXISTS kseaapp_metadata__ppep__idx
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5428 ON kseaapp_metadata(ppep);
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5429 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5430 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5431 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5432 DROP VIEW IF EXISTS v_kseaapp_contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5433 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5434 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5435 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5436 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5437 CREATE VIEW v_kseaapp_contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5438 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5439 SELECT a.*, b.Protein, b.Gene, b.Peptide, b.`Residue.Both`
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5440 FROM v_contrast_log2_fc_p_val a, kseaapp_metadata b
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5441 WHERE b.ppep = a.phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5442 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5443 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5444 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5445 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5446 DROP VIEW IF EXISTS v_kseaapp_input
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5447 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5448 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5449 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5450 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5451 CREATE VIEW v_kseaapp_input
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5452 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5453 SELECT v.contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5454 v.phosphopep,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5455 m.`Protein`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5456 m.`Gene`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5457 m.`Peptide`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5458 m.`Residue.Both`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5459 v.p_value_raw AS `p`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5460 v.log2_fc AS `FC`
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5461 FROM kseaapp_metadata AS m,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5462 v_contrast_log2_fc_p_val AS v
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5463 WHERE m.ppep = v.phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5464 AND NOT m.`Gene` = 'No_Gene_Name'
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5465 AND NOT v.log2_fc = 0
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5466 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5467 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5468 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5469 # We are done with DDL and insertion
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5470 RSQLite::dbDisconnect(db)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5471 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5472 ```
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5473
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5474 ```{r echo = FALSE, results = 'asis'}
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5475 cat("\\newpage\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
5476 ```
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5477
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5478 # KSEA Analysis Summaries
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
5479
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
5480 Results of Kinase-Substrate Enrichment Analysis are presented here, if the substrates for any kinases are relatively enriched. Enrichments are found by the CRAN `KSEAapp` package:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5481
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5482 - The package is available on CRAN, at https:/cran.r-project.org/package=KSEAapp
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
5483 - The method used is described in Casado et al. (2013) [doi:10.1126/scisignal.2003573](https:/doi.org/10.1126/scisignal.2003573) and Wiredja et al (2017) [doi:10.1093/bioinformatics/btx415](https:/doi.org/10.1093/bioinformatics/btx415).
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5484 - An online alternative (supporting only analysis of human data) is available at [https:/casecpb.shinyapps.io/ksea/](https:/casecpb.shinyapps.io/ksea/).
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5485
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5486 For each kinase, $i$, and each two-way contrast of treatments, $j$, an enrichment $z$-score is computed as:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5487
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5488 $$
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5489 \text{kinase enrichment }z\text{-score}_{j,i} = \frac{(\overline{`r sfc`}_{j,i} - \overline{`r pfc`}_j)\sqrt{m_{j,i}}}{\delta_j}
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5490 $$
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5491
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5492 and fold-enrichment is computed as:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5493
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5494 $$
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5495 \text{Enrichment}_{j,i} = \frac{\overline{`r sfc`}_{j,i}}{\overline{`r pfc`}_j}
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5496 $$
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5497
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5498 where:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5499
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5500 - $\overline{`r sfc`}_{j,i}$ is the mean `r pfc_txt` in intensities of known substrates of the kinase $i$ in contrast $j$,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5501 - $\overline{`r pfc`}_j$ is the mean `r pfc_txt` of all phosphosites identified in contrast $j$, and
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5502 - $m_{j,i}$ is the total number of phosphosite substrates of kinase $i$ identified in contrast $j$,
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5503 - $\delta_j$ is the standard deviation of the $\log_2 (\text{fold-change})$ for contrast $j$ across all phosphosites in the dataset.
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5504 - Note that the absolute value of fold-change is used so that both increased and decreased substrates of a kinase will contribute to its enrichment score.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5505
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5506 $\text{FDR}_{j,i}$ is the False Discovery Rate corrected kinase enrichment score.
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5507
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5508 Color intensity in heatmaps reflects magnitude of $z$-score for enrichment of respective kinase in respective contrast; hue reflects the sign of the $z$-score (blue, negative; red, positive).
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5509
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5510 Asterisks in heatmaps reflect enrichments that are significant at `r ksea_cutoff_statistic` < `r ksea_cutoff_threshold`.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5511
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5512 - Kinase names are generally as presented at Phospho.ELM [http://phospho.elm.eu.org/kinases.html](http://phospho.elm.eu.org/kinases.html) (when available), although Phospho.ELM data are not yet incorporated into this analysis.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5513 - Kinase names having the suffix '(HPRD)' are as presented at [http://hprd.org/serine_motifs](http://hprd.org/serine_motifs) and [http://hprd.org/tyrosine_motifs](http://hprd.org/tyrosine_motifs) and are as originally reported in the Amanchy et al., 2007 (doi: [10.1038/nbt0307-285](https://doi.org/10.1038/nbt0307-285)).
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5514 - Kinase-substrate data were also taken from [http://networkin.science/download.shtml](http://networkin.science/download.shtml) and from PhosphoSitePlus [https://www.phosphosite.org/staticDownloads](https://www.phosphosite.org/staticDownloads).
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5515
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5516 For each enriched kinase, a heatmap showing the intensities is presented for up to `r g_intensity_hm_rows` substrates, i.e., those substrates having the highest"quality".
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5517
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5518 Where possible, a heatmap of the correlations among these the selected substrates is also presented; if correlations cannot be computed (because of too many missing values), then the covariances are heatmapped for substrates having a variance greater than 1.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5519
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5520 ```{r ksea, echo = FALSE, fig.dim = c(12, 14.5), results = 'asis'}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5521 cat("\\clearpage\n")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5522
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5523 db <- RSQLite::dbConnect(RSQLite::SQLite(), ksea_app_prep_db)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5524
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5525 # -- eliminate the table that's about to be defined
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5526 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5527 DROP TABLE IF EXISTS site_metadata;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5528 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5529
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5530 # -- define the site_metadata table
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5531 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5532 CREATE TABLE site_metadata(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5533 id INTEGER PRIMARY KEY
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
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diff changeset
5534 , site_type_id INTEGER REFERENCES site_type(id)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5535 , full TEXT UNIQUE ON CONFLICT IGNORE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5536 , abbrev TEXT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5537 , pattern TEXT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5538 , motif TEXT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5539 );
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5540 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5541
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5542 # -- populate the table with initial values
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5543 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5544 INSERT INTO site_metadata(full, abbrev, site_type_id)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5545 SELECT DISTINCT kinase_map, kinase_map, site_type_id
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5546 FROM ppep_gene_site
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5547 ORDER BY kinase_map;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5548 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5549
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5550 # -- drop bogus KSData view if exists
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5551 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5552 DROP VIEW IF EXISTS ks_data_v;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5553 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5554
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5555 # -- create view to serve as an impostor for KSEAapp::KSData
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5556 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5557 CREATE VIEW IF NOT EXISTS ks_data_v
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5558 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5559 SELECT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5560 'NA' AS KINASE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5561 'NA' AS KIN_ACC_ID,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5562 kinase_map AS GENE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5563 'NA' AS KIN_ORGANISM,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5564 'NA' AS SUBSTRATE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5565 0 AS SUB_GENE_ID,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5566 'NA' AS SUB_ACC_ID,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5567 gene_names AS SUB_GENE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5568 'NA' AS SUB_ORGANISM,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5569 phospho_peptide AS SUB_MOD_RSD,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5570 0 AS SITE_GROUP_ID,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5571 'NA' AS 'SITE_7AA',
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5572 2 AS networkin_score,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5573 type_name AS Source
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5574 FROM ppep_gene_site_view;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5575 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5576
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5577 contrast_metadata_df <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5578 sqldf::sqldf("select * from contrast_lvl_lvl_metadata", connection = db)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5579 rslt <- new_env()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5580 rslt$score_list <- list()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5581 rslt$name_list <- list()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5582 rslt$longname_list <- list()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5583
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5584 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5585 DROP TABLE IF EXISTS contrast_ksea_scores;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5586 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5587 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5588
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5589 next_index <- 0
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5590 err_na_subscr_df_const <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5591 "missing values are not allowed in subscripted assignments of data frames"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5592
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5593 for (i_cntrst in seq_len(nrow(contrast_metadata_df))) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5594 cntrst_a_level <- contrast_metadata_df[i_cntrst, "a_level"]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5595 cntrst_b_level <- contrast_metadata_df[i_cntrst, "b_level"]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5596 cntrst_fold_change <- contrast_metadata_df[i_cntrst, 6]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5597 contrast_label <- sprintf("%s -> %s", cntrst_b_level, cntrst_a_level)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5598 contrast_longlabel <- (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5599 sprintf(
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
5600 "Class %s -> Class %s",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5601 contrast_metadata_df[i_cntrst, "b_level"],
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
5602 contrast_metadata_df[i_cntrst, "a_level"]
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5603 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5604 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5605 kseaapp_input <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5606 sqldf::sqldf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5607 x = sprintf("
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5608 SELECT `Protein`, `Gene`, `Peptide`, phosphopep AS `Residue.Both`, `p`, `FC`
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5609 FROM v_kseaapp_input
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5610 WHERE contrast = %d
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5611 ",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5612 i_cntrst
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5613 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5614 connection = db
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5615 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5616
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5617 pseudo_ksdata <- dbReadTable(db, "ks_data_v")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5618
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5619 # This hack is because SQL table has the log2-transformed values
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5620 kseaapp_input[, "FC"] <- 2 ** kseaapp_input[, "FC", drop = TRUE]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5621 main_title <- (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5622 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5623 "Change from treatment %s to treatment %s",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5624 contrast_metadata_df[i_cntrst, "b_level"],
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5625 contrast_metadata_df[i_cntrst, "a_level"]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5626 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5627 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5628 sub_title <- contrast_longlabel
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5629 tryCatch(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5630 expr = {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5631 ksea_scores_rslt <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5632 ksea_scores(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5633 ksdata = pseudo_ksdata,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5634 px = kseaapp_input,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5635 networkin = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5636 networkin_cutoff = 2,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5637 minimum_substrate_count = ksea_min_substrate_count
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5638 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5639
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5640 if (FALSE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5641 ksea_scores_rslt <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5642 ksea_scores_rslt[
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5643 ksea_scores_rslt$m >= ksea_min_substrate_count,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5644 ,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5645 drop = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5646 ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5647 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5648
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5649 if (FALSE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5650 data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5651 x = ksea_scores_rslt,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5652 tabstops = c(0.8, 0.8, 0.8, 0.8, 0.8, 0.8),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5653 caption = paste("KSEA scores for contrast ",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5654 cntrst_b_level, "to", cntrst_a_level),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5655 use_subsubsection_header = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5656 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5657 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5658
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5659 if (FALSE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5660 if (print_nb_messages) nbe("Output contents of `ksea_scores_rslt` table\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5661 cat_variable(ksea_scores_rslt)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5662 cat("\n\\clearpage\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5663 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5664
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5665 if (0 < sum(!is.nan(ksea_scores_rslt$FDR))) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5666 next_index <- 1 + next_index
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5667 rslt$score_list[[next_index]] <- ksea_scores_rslt
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5668 rslt$name_list[[next_index]] <- contrast_label
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5669 rslt$longname_list[[next_index]] <- contrast_longlabel
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5670 ksea_low_fdr_print(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5671 rslt = rslt,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5672 i_cntrst = i_cntrst,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5673 i = next_index,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5674 a_level = cntrst_a_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5675 b_level = cntrst_b_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5676 fold_change = cntrst_fold_change,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5677 caption = contrast_longlabel
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5678 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5679 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5680 },
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5681 error = function(e) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5682 str(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5683 cat_margins()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5684 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5685 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5686 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5687
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5688 plotted_kinases <- NULL
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5689 if (g_can_run_ksea && length(rslt$score_list) > 1) {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5690 for (i in seq_len(length(ksea_heatmap_titles))) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5691 hdr <- ksea_heatmap_titles[[i]]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5692 which_kinases <- i
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5693
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5694 cat("\\clearpage\n\\begin{center}\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5695 if (i == const_ksea_astrsk_kinases) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5696 cat(subsection_header(hdr))
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5697 } else {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5698 cat(subsection_header(hdr))
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5699 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5700 cat("\\end{center}\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5701
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5702 plotted_kinases <- ksea_heatmap(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5703 # the data frame outputs from the KSEA.Scores() function, in list format
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5704 score_list = rslt$score_list,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5705 # a character vector of all the sample names for heatmap annotation:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5706 # - the names must be in the same order as the data in score_list
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5707 # - please avoid long names, as they may get cropped in the final image
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5708 sample_labels = rslt$name_list,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5709 # character string of either "p.value" or "FDR" indicating the data column
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5710 # to use for marking statistically significant scores
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5711 stats = c("p.value", "FDR")[2],
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5712 # a numeric value between 0 and infinity indicating the min. number of
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5713 # substrates a kinase must have to be included in the heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5714 m_cutoff = 1,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5715 # a numeric value between 0 and 1 indicating the p-value/FDR cutoff
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5716 # for indicating significant kinases in the heatmap
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5717 p_cutoff = params$kseaCutoffThreshold,
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5718 # a binary input of TRUE or FALSE, indicating whether or not to perform
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5719 # hierarchical clustering of the sample columns
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5720 sample_cluster = TRUE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5721 # a binary input of TRUE or FALSE, indicating whether or not to export
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5722 # the heatmap as a .png image into the working directory
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5723 export = FALSE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5724 # additional arguments to gplots::heatmap.2, such as:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5725 # - main: main title of plot
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5726 # - xlab: x-axis label
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5727 # - ylab: y-axis label
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5728 xlab = "Contrast",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5729 ylab = "Kinase",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5730 # print which kinases:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
5731 # - 1 : all kinases
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5732 # - 2 : significant kinases
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
5733 # - 3 : non-significant kinases
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5734 which_kinases = which_kinases,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5735 margins = c(7, 15)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5736 )
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
5737 if (!is.null(plotted_kinases)) {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
5738 cat("\\begin{center}\n")
25
f9cd87ac8006 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c58b9b301977f191acd40a22b630177c381317ca
eschen42
parents: 24
diff changeset
5739 if (which_kinases != const_ksea_nonastrsk_kinases)
f9cd87ac8006 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c58b9b301977f191acd40a22b630177c381317ca
eschen42
parents: 24
diff changeset
5740 cat("Asterisks reflect significance.\n")
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
5741 cat("\\end{center}\n")
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
5742 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5743 } # end for (i in ...
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5744 } # end if (length ...
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5745 ```
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5746
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5747 ```{r kseabar_calc, echo = FALSE, fig.dim = c(9.5, 6), results = 'asis'}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5748 ksea_prints <- list()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5749 ksea_barplots <- list()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5750 for (i_cntrst in seq_len(length(rslt$score_list))) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5751 next_index <- i_cntrst
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5752 cntrst_a_level <- contrast_metadata_df[i_cntrst, "a_level"]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5753 cntrst_b_level <- contrast_metadata_df[i_cntrst, "b_level"]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5754 cntrst_fold_change <- contrast_metadata_df[i_cntrst, 6]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5755 contrast_label <- sprintf("%s -> %s", cntrst_b_level, cntrst_a_level)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5756 contrast_longlabel <- (
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5757 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5758 "Class %s -> Class %s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5759 contrast_metadata_df[i_cntrst, "b_level"],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5760 contrast_metadata_df[i_cntrst, "a_level"]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5761 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5762 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5763 main_title <- (
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5764 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5765 "Change from treatment %s to treatment %s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5766 contrast_metadata_df[i_cntrst, "b_level"],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5767 contrast_metadata_df[i_cntrst, "a_level"]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5768 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5769 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5770 sub_title <- contrast_longlabel
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5771 tryCatch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5772 expr = {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5773 ksea_scores_rslt <- rslt$score_list[[next_index]]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5774 if (print_nb_messages) nbe(see_variable(ksea_scores_rslt)) #ACE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5775
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5776 if (0 < sum(!is.nan(ksea_scores_rslt$FDR))) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5777 sink(deferred <- file())
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5778 ksea_low_fdr_print(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5779 rslt = rslt,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5780 i_cntrst = i_cntrst,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5781 i = next_index,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5782 a_level = cntrst_a_level,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5783 b_level = cntrst_b_level,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5784 fold_change = cntrst_fold_change,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5785 caption = contrast_longlabel,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5786 write_db = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5787 anchor = const_table_anchor_t
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5788 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5789 cat("\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5790 sink()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5791 lines <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5792 paste(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5793 readLines(deferred, warn = FALSE),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5794 collapse = "\n"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5795 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5796 close(deferred)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5797 sq_put(ksea_prints, lines)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5798 sink(stderr())
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5799 cat("\n---\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5800 cat_variable(ksea_prints)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5801 barplot_closure <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5802 ksea_low_fdr_barplot_factory(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5803 rslt = rslt,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5804 i_cntrst = i_cntrst,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5805 i = next_index,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5806 a_level = cntrst_a_level,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5807 b_level = cntrst_b_level,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5808 fold_change = cntrst_fold_change,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5809 caption = contrast_longlabel
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5810 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5811 if (rlang::is_closure(barplot_closure))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5812 sq_put(ksea_barplots, barplot_closure)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5813 else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5814 sq_put(ksea_barplots, no_op)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5815 str(ksea_barplots)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5816 cat("\n...\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5817 sink()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5818 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5819 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5820 error = function(e) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5821 str(e)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5822 cat_margins()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5823 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5824 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5825 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5826 ```
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5827
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5828 ```{r phosphoelm_kinase_upid_desc, echo = FALSE, fig.dim = c(12, 13.7), results = 'asis'}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5829
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5830 have_kinase_descriptions <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5831 if (!is.null(bzip2df(kinase_uprt_desc_lut, kinase_uprt_desc_lut_bz2)) &&
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5832 !is.null(bzip2df(kinase_name_uprt_lut, kinase_name_uprt_lut_bz2))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5833 ) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5834 rownames(kinase_uprt_desc_lut) <- kinase_uprt_desc_lut$UniProtID
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5835 kinase_name_to_desc_uprt <- function(s) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5836 rslt <- NULL
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5837 tryCatch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5838 {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5839 which_rows <- eval(s == kinase_name_uprt_lut$kinase)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5840 kinase_uprtid <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5841 kinase_name_uprt_lut[which_rows, 2]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5842 # filter for first _HUMAN match if any
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5843 grepl_human <- grepl("_HUMAN$", kinase_uprtid)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5844 if (0 < sum(grepl_human))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5845 kinase_uprtid <- kinase_uprtid[grepl_human]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5846 # filter for first match if any
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5847 if (0 < length(kinase_uprtid)) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5848 kinase_uprtid <- kinase_uprtid[1]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5849 kinase_desc <- kinase_uprt_desc_lut[kinase_uprtid, 2]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5850 if (!is.na(kinase_desc))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5851 rslt <- c(kinase_desc, kinase_uprtid)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5852 else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5853 rslt <- c(kinase_desc, "")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5854 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5855 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5856 warning = str
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5857 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5858 rslt
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5859 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5860 TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5861 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5862 kinase_name_to_desc_uprt <- function(s) NULL
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5863 FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5864 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5865 ```
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5866
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5867 ```{r write_params, echo = FALSE, results = 'asis'}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5868 # perhaps this should be moved into the functions section, eventually ...
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5869 write_params <- function(db) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5870 # write parameters to report
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5871
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5872 # write parameters to SQLite output
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5873
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5874 mqppep_anova_script_param_df <- data.frame(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5875 script = "mqppep_anova_script.Rmd",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5876 parameter = names(param_unlist),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5877 value = param_unlist
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5878 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5879 ddl_exec(db, "
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5880 DROP TABLE IF EXISTS script_parameter;
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5881 "
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5882 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5883 ddl_exec(db, "
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5884 CREATE TABLE IF NOT EXISTS script_parameter(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5885 script TEXT,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5886 parameter TEXT,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5887 value ANY,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5888 UNIQUE (script, parameter) ON CONFLICT REPLACE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5889 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5890 ;
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5891 "
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5892 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5893 RSQLite::dbWriteTable(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5894 conn = db,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5895 name = "script_parameter",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5896 value = mqppep_anova_script_param_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5897 append = TRUE
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5898 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5899
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5900 loaded_packages_df <- sessioninfo::package_info("loaded")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5901 loaded_packages_df[, "library"] <- as.character(loaded_packages_df$library)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5902 loaded_packages_df <- data.frame(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5903 package = loaded_packages_df$package,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5904 version = loaded_packages_df$loadedversion,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5905 date = loaded_packages_df$date
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5906 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5907 #ACE cat("\\clearpage\n\\section{R package versions}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5908 #ACE data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5909 #ACE x = loaded_packages_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
5910 #ACE tabstops = c(2.5, 1.25),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5911 #ACE caption = "R package versions"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5912 #ACE )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5913 cat("\\clearpage\n\\section{Input parameter settings}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5914 data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5915 x = param_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5916 tabstops = c(1.75),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
5917 underscore_whack = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5918 caption = "Input parameters",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5919 verbatim = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5920 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5921 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5922
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5923 if (!have_kinase_descriptions) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5924 write_params(db)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5925 # We are done with output
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5926 RSQLite::dbDisconnect(db)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5927 param_df_exit()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5928 knitr::knit_exit()
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5929 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5930 ```
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
5931
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5932 ```{r kseabar, echo = FALSE, fig.dim = c(9.5, 12.3), results = 'asis'}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5933 if (have_kinase_descriptions) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5934 my_section_header <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5935 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5936 "inases whose KSEA %s < %s\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5937 ksea_cutoff_statistic,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5938 signif(ksea_cutoff_threshold, 2)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5939 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5940
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5941 # Use enriched kinases to find enriched kinase-substrate pairs
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5942 enriched_kinases <- data.frame(kinase = ls(ksea_asterisk_hash))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5943
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5944 enriched_kinase_descs <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5945 Reduce(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5946 f = function(l, r) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5947 lkup <- kinase_name_to_desc_uprt(r)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5948 if (is.null(lkup)) l
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5949 else r2 <- rbind(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5950 l,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5951 data.frame(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5952 kinase = r,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5953 uniprot_id = lkup[2],
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5954 description = lkup[1]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5955 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5956 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5957 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5958 x = enriched_kinases$kinase,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5959 init = NULL
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5960 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5961
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5962 if (length(enriched_kinase_descs) > 0 && nrow(enriched_kinase_descs) > 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5963 cat("\n\\clearpage\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5964 data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5965 x = enriched_kinase_descs,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5966 tabstops = c(0.9, 1.3),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5967 headings = c("Kinase", "UniProt ID", "Description"),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5968 caption = paste0("Descriptions of k", my_section_header)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5969 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5970 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5971
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5972 if (FALSE) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5973 cat_variable(sqldf("SELECT kinase FROM enriched_kinases"))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5974 cat_variable(sqldf("
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5975 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5976 FROM pseudo_ksdata
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5977 WHERE gene IN (SELECT kinase FROM enriched_kinases)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5978 "))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5979 data_frame_table_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5980 x = sqldf("
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5981 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5982 FROM pseudo_ksdata
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5983 WHERE gene IN (SELECT kinase FROM enriched_kinases)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5984 "),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5985 justification = "l l l",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5986 centered = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5987 caption = "substrates of enriched kinases",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5988 anchor = c(const_table_anchor_p, const_table_anchor_t),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5989 underscore_whack = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5990 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5991 data_frame_table_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5992 x = sqldf("
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5993 SELECT
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5994 gene AS kinase,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5995 ppep,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5996 sub_gene,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5997 '('||group_concat(gene||'-'||sub_gene)||') '||ppep AS label,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5998 fdr_adjusted_anova_p,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
5999 quality,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6000 min_group_obs_count
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6001 FROM (
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6002 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6003 FROM pseudo_ksdata
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6004 WHERE gene IN (SELECT kinase FROM enriched_kinases)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6005 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6006 p_value_data
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6007 WHERE ppep = phosphopeptide
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6008 GROUP BY kinase, ppep
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6009 ORDER BY kinase, ppep, p_value_data.quality DESC
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6010 "),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6011 justification = "l l l l l l l",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6012 centered = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6013 caption = "labeled substrates of enriched kinases",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6014 anchor = c(const_table_anchor_p, const_table_anchor_t),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6015 underscore_whack = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6016 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6017 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6018 all_enriched_substrates <- sqldf("
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6019 SELECT
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6020 gene AS kinase,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6021 ppep,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6022 sub_gene,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6023 '('||group_concat(gene||'-'||sub_gene)||') '||ppep AS label,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6024 fdr_adjusted_anova_p,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6025 quality,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6026 min_group_obs_count
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6027 FROM (
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6028 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6029 FROM pseudo_ksdata
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6030 WHERE gene IN (SELECT kinase FROM enriched_kinases)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6031 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6032 p_value_data
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6033 WHERE ppep = phosphopeptide
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6034 GROUP BY kinase, ppep
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6035 ORDER BY kinase, ppep, p_value_data.quality DESC
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6036 ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6037
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6038 all_enriched_substrates <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6039 all_enriched_substrates[
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6040 all_enriched_substrates$quality >= params$minQuality,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6041 ,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6042 drop = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6043 ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6044
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6045 all_enriched_substrates$sub_gene <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6046 sub(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6047 " ///.*",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6048 " ...",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6049 all_enriched_substrates$sub_gene
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6050 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6051
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6052 all_enriched_substrates$label <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6053 with(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6054 all_enriched_substrates,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6055 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6056 "(%s-%s) %s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6057 kinase,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6058 trunc_subgene(sub_gene),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6059 ppep
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6060 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6061 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6062
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6063 # this global is set to TRUE by cat_enriched_heading immediately below
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6064 g_neednewpage <- FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6065
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6066 # helper used to label per-kinase substrate enrichment figure
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6067 cat_enriched_heading <- function(m, cut_args) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6068 cutoff <- cut_args$cutoff
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6069 kinase <- cut_args$kinase
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6070 if (g_neednewpage) cat("\\newpage\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6071 g_neednewpage <- TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6072 if (nrow(m) > g_intensity_hm_rows) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6073 cat(subsection_header(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6074 sprintf(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6075 "Highest-quality %d (of %d) enriched %s-substrates",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6076 g_intensity_hm_rows,
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6077 nrow(m),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6078 kinase
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6079 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6080 ))
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6081 } else {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6082 if (nrow(m) == 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6083 return(FALSE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6084 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6085 nrow_m <- nrow(m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6086 cat(subsection_header(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6087 sprintf(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6088 "%d enriched %s-substrate%s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6089 nrow_m,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6090 kinase,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6091 if (nrow_m > 1) "s" else ""
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6092 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6093 ))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6094 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6095 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6096 cat("\n\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6097 cat("\n\n\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6098 return(TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6099 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6100
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6101 # --------------------------------
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6102 # hack begin - show all substrates
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6103 enriched_substrates <- all_enriched_substrates
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6104 # add "FALSE &&" to prevent listing of substrates
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6105 if (show_enriched_substrates && nrow(enriched_substrates) > 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6106 short_row_names <- sub(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6107 "$FAILED_MATCH_GENE_NAME",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6108 "not_found",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6109 enriched_substrates$sub_gene,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6110 fixed = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6111 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6112
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6113 if (print_nb_messages) nbe(see_variable(enriched_substrates))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6114 substrates_df <- with(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6115 enriched_substrates,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6116 data.frame(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6117 kinase = kinase,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6118 substrate = sub(" ///*", "...", short_row_names),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6119 anova_p_value = signif(fdr_adjusted_anova_p, 2),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6120 min_group_obs_count = signif(min_group_obs_count, 0),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6121 quality = signif(quality, 3),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6122 sequence = trunc_n(30)(ppep)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6123 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6124 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6125
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6126 substrates_df <- substrates_df[
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6127 with(substrates_df, order(kinase, -quality)),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6128 ,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6129 drop = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6130 ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6131
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6132 if (print_nb_messages) nbe(see_variable(substrates_df))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6133 if (nrow(substrates_df) < 1)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6134 substrates_df$sequence <- c()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6135 if (print_nb_messages) nbe(see_variable(substrates_df))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6136 names(substrates_df) <- headers_2nd_line <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6137 c("Kinase", "Substrate", "p-value", "per group)", "quality", "Sequence")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6138 headers_1st_line <- c("", "", "ANOVA", "min(values", "", "")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6139 data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6140 x = substrates_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6141 tabstops = c(1.2, 0.8, 0.5, 0.65, 0.5),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6142 headings = c(headers_1st_line, headers_2nd_line),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6143 caption = "Details for all enriched substrates of enriched kinases"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6144 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6145 rm(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6146 enriched_substrates,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6147 substrates_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6148 short_row_names,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6149 headers_1st_line,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6150 headers_2nd_line
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6151 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6152 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6153 cat("\\clearpage\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6154 # hack end - show all substrates
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6155 # --------------------------------
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6156
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6157 # print deferred tables and graphs for kinases from contrasts
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6158 for (i_cntrst in seq_len(length(ksea_prints))) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6159 #latex_samepage({
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6160 cat(ksea_prints[[i_cntrst]])
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6161 cat("\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6162 ksea_barplots[[i_cntrst]]()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6163 cat("\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6164 cat("\\clearpage\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6165 #})
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6166 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6167
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6168 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6169 ```
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6170
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6171 ```{r enriched, echo = FALSE, fig.dim = c(12, 13.7), results = 'asis'}
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6172 if (g_can_run_ksea) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6173 g_did_enriched_header <- FALSE
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6174 for (kinase_name in sort(enriched_kinases$kinase)) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6175 enriched_substrates <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6176 all_enriched_substrates[
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6177 all_enriched_substrates$kinase == kinase_name,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6178 ,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6179 drop = FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6180 ]
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6181 ten_trunc_ppep <- trunc_enriched_substrate(enriched_substrates$ppep)
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
6182 enriched_substrates$label <- with(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents: 22
diff changeset
6183 enriched_substrates,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
6184 sprintf(
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6185 "(%s) %s",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6186 make.names(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6187 sub("$FAILED_MATCH_GENE_NAME", "not_found", sub_gene, fixed = TRUE),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6188 unique = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6189 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6190 ten_trunc_ppep
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents: 22
diff changeset
6191 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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parents: 22
diff changeset
6192 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6193 # Get the intensity values for the heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6194 enriched_intensities <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6195 as.matrix(unimputed_quant_data_log[enriched_substrates$ppep, , drop = FALSE])
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6196
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6197 # Remove rows having too many NA values to be relevant
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6198 good_rows <- (rowSums(enriched_intensities, na.rm = TRUE) != 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6199 #ACE nbe(see_variable(good_rows), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6200 enriched_substrates <- enriched_substrates[good_rows, , drop = FALSE]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6201 enriched_intensities <- enriched_intensities[good_rows, , drop = FALSE]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6202
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6203 # Rename the rows with the display-name for the heatmap
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6204 short_row_names <- sub(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6205 "$FAILED_MATCH_GENE_NAME",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6206 "not_found",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6207 enriched_substrates$sub_gene,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6208 fixed = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6209 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6210 short_row_names <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6211 make.names(short_row_names, unique = TRUE)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6212 long_row_names <-
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6213 sapply(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6214 X = rownames(enriched_intensities),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6215 FUN = function(rn) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6216 enriched_substrates[enriched_substrates$ppep == rn, "label"]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6217 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6218 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6219 rownames(enriched_intensities) <- long_row_names
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6220 # Format as matrix for heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6221 m <- as.matrix(enriched_intensities)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6222 rownames(m) <- trunc_enriched_substrate(rownames(m))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6223
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6224 #ACE nb("m with bad rows: ", see_variable(m), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6225 #ACE good_rows <- (rowSums(m, na.rm = TRUE) != 0)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6226 #ACE nb(see_variable(good_rows), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6227 #ACE m <- m[good_rows, , drop = FALSE]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6228 #ACE nb("m without(?) bad rows: ", see_variable(m), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6229 #ACE nb(see_variable(short_row_names), "\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6230 #ACE local_short_row_names <- short_row_names[good_rows]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6231 #ACE local_long_row_names <- long_row_names[good_rows]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6232 #ACE local_enriched_intensities <- enriched_intensities[local_long_row_names, ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6233
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6234 # Draw the heading and heatmap
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6235 nrow_m <- nrow(m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6236 if (nrow_m > 0) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6237 if (!g_did_enriched_header) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6238 cat("\n\\clearpage\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6239 cat(section_header(paste0("K", my_section_header)))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6240 g_did_enriched_header <- TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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parents: 25
diff changeset
6241 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6242 is_na_m <- is.na(m)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6243 cellnote_m <- is_na_m
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6244 cellnote_m[!is_na_m] <- ""
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6245 cellnote_m[is_na_m] <- "NA"
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6246 cut_args <- new_env()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6247 cut_args$cutoff <- cutoff
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6248 cut_args$kinase <- kinase_name
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6249 cut_args$statistic <- ksea_cutoff_statistic
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6250 cut_args$threshold <- ksea_cutoff_threshold
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6251 number_of_peptides_found <-
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6252 ppep_heatmap(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6253 m = m,
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6254 cellnote = cellnote_m,
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6255 cutoff = cut_args,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6256 hm_heading_function = cat_enriched_heading,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6257 hm_main_title
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6258 = "Unnormalized (zero-imputed) intensities of enriched kinase-substrates",
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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diff changeset
6259 suppress_row_dendrogram = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6260 master_cex = 0.35,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6261 sepcolor = "black",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6262 colsep = sample_colsep
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6263 )
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
6264 if (number_of_peptides_found > 1) {
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6265
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6266 tryCatch(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6267 {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6268 rownames(m) <- short_row_names
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6269 cov_heatmap(m, nrow_m > g_intensity_hm_rows)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6270 },
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6271 error = function(e) {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6272 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6273 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6274 "ERROR: %s\n\\newline\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6275 mget("e")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6276 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6277 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6278 cat(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6279 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6280 "message: %s\n\\newline\n",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6281 e$message
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6282 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6283 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6284 cat_margins()
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6285 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6286 )
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
6287 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6288 substrates_df <- with(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6289 enriched_substrates,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6290 data.frame(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6291 substrate = sub(" ///*", "...", short_row_names),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6292 sequence = trunc_long_ppep(ppep),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6293 anova_p_value = signif(fdr_adjusted_anova_p, 2),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6294 min_group_obs_count = signif(min_group_obs_count, 0),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6295 quality = signif(quality, 3)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6296 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6297 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6298 excess_substrates <- nrow(substrates_df) > g_intensity_hm_rows
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6299 if (excess_substrates)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6300 substrates_df <- substrates_df[1:g_intensity_hm_rows, ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6301 names(substrates_df) <- headers_2nd_line <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6302 c("Substrate", "Sequence", "p-value", "per group)", "quality")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6303 headers_1st_line <- c("", "", "ANOVA", "min(values", "")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6304 if (1 < nrow(enriched_substrates))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6305 cat("\n\\newpage\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6306 cat(subsubsection_header(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6307 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6308 "Details for %s%s-substrates",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6309 if (excess_substrates)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6310 sprintf(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6311 "%s \"highest quality\" ",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6312 g_intensity_hm_rows
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
6313 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6314 else "",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6315 kinase_name
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
6316 )
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6317 ))
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6318 substrates_df <- substrates_df[order(-substrates_df$quality), ]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6319 data_frame_tabbing_latex(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6320 x = substrates_df,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6321 tabstops = c(0.8, 3.8, 0.6, 0.8),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6322 headings = c(headers_1st_line, headers_2nd_line)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6323 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6324 } else {
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6325 if (print_nb_messages) nbe(see_variable(nrow_m > 0), "\n")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6326 }
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6327 if (print_nb_messages) nb("end kinase ", kinase_name, "\n")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6328 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6329
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6330 # Write output tabular files
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6331
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6332 # get kinase, ppep, concat(kinase) tuples for enriched kinases
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6333
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6334 if (print_nb_messages) nb("kinase_ppep_label <- ...\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6335 if (print_nb_messages) nbe("kinase_ppep_label <- ...\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6336 kinase_ppep_label <- sqldf("
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6337 WITH
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6338 t(ppep, label) AS
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6339 (
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6340 SELECT DISTINCT
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6341 SUB_MOD_RSD AS ppep,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6342 group_concat(gene, '; ') AS label
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6343 FROM pseudo_ksdata
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6344 WHERE GENE IN (SELECT kinase FROM enriched_kinases)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6345 GROUP BY ppep
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6346 ),
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6347 k(kinase, ppep_join) AS
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6348 (
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6349 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep_join
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6350 FROM pseudo_ksdata
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6351 WHERE GENE IN (SELECT kinase FROM enriched_kinases)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6352 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6353 SELECT k.kinase, t.ppep, t.label
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6354 FROM t, k
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6355 WHERE t.ppep = k.ppep_join
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6356 ORDER BY k.kinase, t.ppep
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6357 ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6358
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6359
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6360 # extract what we need from full_data
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6361 impish <- cbind(rownames(quant_data_imp), quant_data_imp)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6362 colnames(impish)[1] <- "Phosphopeptide"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6363 data_table_imputed_sql <- "
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6364 SELECT
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6365 f.*,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6366 k.label AS KSEA_enrichments,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6367 q.*
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6368 FROM
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6369 metadata_plus_p f
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6370 LEFT JOIN kinase_ppep_label k
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6371 ON f.Phosphopeptide = k.ppep,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6372 impish q
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6373 WHERE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6374 f.Phosphopeptide = q.Phosphopeptide
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6375 "
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6376 data_table_imputed <- sqldf(data_table_imputed_sql)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6377 # Zap the duplicated 'Phosphopeptide' column named 'ppep'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6378 data_table_imputed <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6379 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6380
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6381 # Output imputed, un-normalized data
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6382 if (print_nb_messages) nb("Output imputed, un-normalized data tabular file\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6383 if (print_nb_messages) nbe("Output imputed, un-normalized data tabular file\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6384 write.table(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6385 data_table_imputed
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6386 , file = imputed_data_filename
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6387 , sep = "\t"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6388 , col.names = TRUE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6389 , row.names = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6390 , quote = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6391 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6392
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6393
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6394 #output quantile normalized data
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6395 impish <- cbind(rownames(quant_data_imp_qn_log), quant_data_imp_qn_log)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6396 colnames(impish)[1] <- "Phosphopeptide"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6397 data_table_imputed <- sqldf(data_table_imputed_sql)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6398 # Zap the duplicated 'Phosphopeptide' column named 'ppep'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6399 data_table_imputed <-
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6400 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6401 if (print_nb_messages) nb("Output quantile normalized data tabular file\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6402 if (print_nb_messages) nbe("Output quantile normalized data tabular file\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6403 write.table(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6404 data_table_imputed,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6405 file = imp_qn_lt_data_filenm,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6406 sep = "\t",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6407 col.names = TRUE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6408 row.names = FALSE,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6409 quote = FALSE
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6410 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6411
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6412 ppep_kinase <- sqldf("
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6413 SELECT DISTINCT k.ppep, k.kinase
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6414 FROM (
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6415 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6416 FROM pseudo_ksdata
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6417 WHERE GENE IN (SELECT kinase FROM enriched_kinases)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6418 ) k
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6419 ORDER BY k.ppep, k.kinase
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6420 ")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6421
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6422 RSQLite::dbWriteTable(
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6423 conn = db,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6424 name = "ksea_enriched_ks",
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6425 value = ppep_kinase,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6426 append = FALSE
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6427 )
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6428 }
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6429
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6430 if (print_nb_messages) nb("RSQLite::dbWriteTable anova_signif\n")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6431
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6432 RSQLite::dbWriteTable(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6433 conn = db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6434 name = "anova_signif",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6435 value = p_value_data,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6436 append = FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6437 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6438
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6439 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6440 DROP VIEW IF EXISTS stats_metadata_v;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6441 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6442 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6443 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6444 CREATE VIEW stats_metadata_v
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6445 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6446 SELECT DISTINCT m.*,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6447 p.raw_anova_p,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6448 p.fdr_adjusted_anova_p,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6449 kek.kinase AS ksea_enrichments
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6450 FROM
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6451 mrgfltr_metadata_view m
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6452 LEFT JOIN anova_signif p
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6453 ON m.phospho_peptide = p.phosphopeptide
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6454 LEFT JOIN ksea_enriched_ks kek
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6455 ON m.phospho_peptide = kek.ppep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6456 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6457 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6458 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6459
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6460 if (print_nb_messages) nb("Output contents of `stats_metadata_v` table to tabular file\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6461 if (print_nb_messages) nbe("Output contents of `stats_metadata_v` table to tabular file\n")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6462 write.table(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6463 dbReadTable(db, "stats_metadata_v"),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6464 file = anova_ksea_mtdt_file,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6465 sep = "\t",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
6466 col.names = TRUE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6467 row.names = FALSE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6468 quote = FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6469 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6470
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6471 cat("\n\\clearpage\n")
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6472
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6473 ```
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6474
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6475 # Data-processing summary flowchart
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6476
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6477 ![Flowchart showing ANOVA and KSEA data-processing steps](KSEA_impl_flowchart.pdf)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6478
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
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diff changeset
6479 ```{r parmlist, echo = FALSE, fig.dim = c(9, 10), results = 'asis'}
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6480 cat("\\leavevmode\n\n\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
6481
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6482 write_params(db)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6483 # We are done with output
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6484 RSQLite::dbDisconnect(db)
26
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6485
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
parents: 25
diff changeset
6486 cat("\\clearpage\n\\section{R package versions}\n")
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
eschen42
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diff changeset
6487 utils::toLatex(utils::sessionInfo())
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
6488 ```