Mercurial > repos > eschen42 > mqppep_anova

annotate mqppep_anova_script.Rmd @ 24:8582a9797c18 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
author eschen42
date Thu, 14 Jul 2022 02:12:33 +0000
parents 61adb8801b73
children f9cd87ac8006
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c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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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 output:
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11 pdf_document:
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12 toc: true
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13 toc_depth: 3
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14 keep_tex: true
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15 header-includes:
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16 - \usepackage{longtable}
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17 - \newcommand\T{\rule{0pt}{2.6ex}} % Top strut
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18 - \newcommand\B{\rule[-1.2ex]{0pt}{0pt}} % Bottom strut
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19 params:
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20 alphaFile: "test-data/alpha_levels.tabular"
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21 inputFile: "test-data/test_input_for_anova.tabular"
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22 preprocDb: "test-data/test_input_for_anova.sqlite"
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23 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
24
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24 regexSampleNames: "\\.\\d+[A-Z]$"
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25 regexSampleGrouping: "\\d+"
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26 show_toc: true
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27 firstDataColumn: "^Intensity[^_]"
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28 imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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29 meanPercentile: 1
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30 sdPercentile: 1.0
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31 imputedDataFilename: "test-data/limbo/imputedDataFilename.txt"
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32 imputedQNLTDataFile: "test-data/limbo/imputedQNLTDataFile.txt"
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33 anovaKseaMetadata: "test-data/limbo/anovaKseaMetadata.txt"
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34 oneWayManyCategories: !r c("aov", "kruskal.test", "oneway.test")[1]
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35 oneWayTwoCategories: !r c("aov", "kruskal.test", "oneway.test")[3]
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36 kseaCutoffStatistic: !r c("p.value", "FDR")[2]
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37 kseaCutoffThreshold: !r c( 0.1, 0.05)[2]
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38 kseaMinKinaseCount: 1
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39 intensityHeatmapRows: 75
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40 ---
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41 <!--
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42 alphaFile: "test-data/alpha_levels.tabular"
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43 inputFile: "test-data/test_input_for_anova.tabular"
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44 preprocDb: "test-data/test_input_for_anova.sqlite"
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45 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
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46 regexSampleNames: "\\.\\d+[A-Z]$"
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47 regexSampleGrouping: "\\d+"
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48
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49 alphaFile: "test-data/alpha_levels.tabular"
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50 inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
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51 preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
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52 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
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53 regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$"
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54 regexSampleGrouping: "\\w+"
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55
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56 kseaCutoffStatistic: !r c("p.value", "FDR")[2]
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57 kseaCutoffThreshold: !r c(0.05, 0.1)[1]
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59 alphaFile: "test-data/alpha_levels.tabular"
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60 inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"
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61 preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"
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62 kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
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63 regexSampleNames: "\\.\\d+[A-Z]$"
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64 regexSampleGrouping: "\\d+"
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66 alphaFile: "test-data/alpha_levels.tabular"
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67 inputFile: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.tabular"
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68 preprocDb: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.sqlite"
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69 kseaAppPrepDb: !r c(":memory:", "test-data/pY_Sites_NancyDu.ksea.sqlite")[2]
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70 regexSampleNames: "\\.\\d+[A-Z]$"
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71 regexSampleGrouping: "\\d+"
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73 alphaFile: "test-data/alpha_levels.tabular"
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74 inputFile: "test-data/pST_Sites_NancyDu.txt.preproc.tabular"
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75 preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"
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76 kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]
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78 inputFile: "test-data/density_failure.preproc_tab.tabular"
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79 kseaAppPrepDb: !r c(":memory:", "mqppep.sqlite")[2]
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80 latex_document: default
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81 -->
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82 ```{r setup, include = FALSE}
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83 #ref for debugging: https://yihui.org/tinytex/r/#debugging
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84 options(tinytex.verbose = TRUE)
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85
0
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86 # ref for parameterizing Rmd document: https://stackoverflow.com/a/37940285
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87 # ref for top and bottom struts: https://tex.stackexchange.com/a/50355
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88 knitr::opts_chunk$set(echo = FALSE, fig.dim = c(9, 10))
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89
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90 # freeze the random number generator so the same results will be produced
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91 # from run to run
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92 set.seed(28571)
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93
22
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94 ### LIBRARIES
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95 library(gplots)
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96 library(DBI)
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97 library(RSQLite)
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98 # Suppress "Warning: no DISPLAY variable so Tk is not available"
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99 suppressWarnings(suppressMessages(library(sqldf)))
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100
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101 # required but not added to search list:
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102 # - DBI
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103 # - RSQLite
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104 # - ggplot2
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105 # - knitr
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106 # - latex2exp
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107 # - preprocessCore
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108 # - reshape2
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109 # - vioplot
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110
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111 ### CONSTANTS
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112
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113 const_parfin <- par("fin")
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114 const_boxplot_fill <- "grey94"
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115 const_stripchart_cex <- 0.5
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116 const_stripsmall_cex <-
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117 sqrt(const_stripchart_cex * const_stripchart_cex / 2)
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118 const_stripchart_jitter <- 0.3
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119 const_write_debug_files <- FALSE
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120 const_table_anchor_bp <- "bp"
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121 const_table_anchor_ht <- "ht"
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122 const_table_anchor_p <- "p"
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123 const_table_anchor_tbp <- "tbp"
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124
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125
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126 const_ksea_astrsk_kinases <- 1
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127 const_ksea_nonastrsk_kinases <- 2
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128 const_ksea_all_kinases <- 3
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129
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130 const_log10_e <- log10(exp(1))
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131
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132 ### FUNCTIONS
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133
22
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134 # from `demo(error.catching)`
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135 ##' Catch *and* save both errors and warnings, and in the case of
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136 ##' a warning, also keep the computed result.
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137 ##'
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138 ##' @title tryCatch both warnings (with value) and errors
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139 ##' @param expr an \R expression to evaluate
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140 ##' @return a list with 'value' and 'warning', where
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141 ##' 'value' may be an error caught.
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142 ##' @author Martin Maechler;
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143 ##' Copyright (C) 2010-2012 The R Core Team
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144 try_catch_w_e <- function(expr) {
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145 wrn <- NULL
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146 # warning handler
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147 w_handler <- function(w) {
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148 wrn <<- w
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149 invokeRestart("muffleWarning")
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150 }
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151 list(
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152 value = withCallingHandlers(
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153 tryCatch(
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154 expr,
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155 error = function(e) e
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156 ),
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157 warning = w_handler
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158 ),
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159 warning = wrn
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160 )
7
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161 }
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162
22
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163
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164 write_debug_file <- function(s) {
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165 if (const_write_debug_files) {
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166 s_path <- sprintf("test-data/%s.txt", deparse(substitute(s)))
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167 print(sprintf("DEBUG writing file %s", spath))
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168 write.table(
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169 s,
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170 file = s_path,
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171 sep = "\t",
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172 col.names = TRUE,
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173 row.names = TRUE,
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174 quote = FALSE
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175 )
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176 }
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177 }
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178
22
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179 # ref: http://adv-r.had.co.nz/Environments.html
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180 # "When creating your own environment, note that you should set its parent
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181 # environment to be the empty environment. This ensures you don't
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182 # accidentally inherit objects from somewhere else."
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183 # Caution: this prevents `with(my_env, expr)` from working when `expr`
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184 # contains anything from the global environment, even operators!
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185 # Hence, `x <- 1; get("x", new_env())` fails by design.
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186 new_env <- function() {
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187 new.env(parent = emptyenv())
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188 }
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189
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190 ### numerical/statistical helper functions
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191
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192 any_nan <- function(x) {
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193 !any(x == "NaN")
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194 }
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195
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196 # determine standard deviation of quantile to impute
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197 sd_finite <- function(x) {
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198 ok <- is.finite(x)
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199 sd(x[ok])
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200 }
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201
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202 anova_func <- function(x, grouping_factor, one_way_f) {
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203 subject <- data.frame(
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204 intensity = x
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205 )
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206 x_aov <-
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207 one_way_f(
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208 formula = intensity ~ grouping_factor,
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209 data = subject
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210 )
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211 pvalue <-
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212 if (identical(one_way_f, aov))
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213 summary(x_aov)[[1]][["Pr(>F)"]][1]
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214 else
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215 pvalue <- x_aov$p.value
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216 pvalue
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217 }
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218
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219
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220 ### LaTeX functions
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221
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222 latex_collapsed_vector <- function(collapse_string, v, underscore_whack = TRUE) {
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223 v_sub <- if (underscore_whack) gsub("_", "\\\\_", v) else v
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224 cat(
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225 paste0(
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226 v_sub,
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227 collapse = collapse_string
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228 )
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229 )
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230 }
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231
22
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232 latex_itemized_collapsed <- function(collapse_string, v, underscore_whack = TRUE) {
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233 cat("\\begin{itemize}\n\\item ")
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234 latex_collapsed_vector(collapse_string, v, underscore_whack)
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235 cat("\n\\end{itemize}\n")
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236 }
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237
22
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238 latex_itemized_list <- function(v, underscore_whack = TRUE) {
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239 latex_itemized_collapsed("\n\\item ", v, underscore_whack)
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240 }
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241
22
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242 latex_enumerated_collapsed <- function(collapse_string, v, underscore_whack = TRUE) {
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243 cat("\\begin{enumerate}\n\\item ")
22
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244 latex_collapsed_vector(collapse_string, v, underscore_whack)
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245 cat("\n\\end{enumerate}\n")
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246 }
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247
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248 latex_enumerated_list <- function(v) {
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249 latex_enumerated_collapsed("\n\\item ", v)
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250 }
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251
22
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252 latex_table_row <- function(v, extra = "", underscore_whack = TRUE) {
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253 latex_collapsed_vector(" & ", v, underscore_whack)
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254 cat(extra)
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255 cat(" \\\\\n")
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256 }
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257
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258 # Use this like print.data.frame, from which it is adapted:
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259 data_frame_latex <-
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260 function(
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diff changeset
261 x,
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262 ...,
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263 # digits to pass to format.data.frame
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264 digits = NULL,
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265 # TRUE -> right-justify columns; FALSE -> left-justify
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266 right = TRUE,
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267 # maximumn number of rows to print
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268 max = NULL,
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269 # string with justification of each column
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270 justification = NULL,
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271 # TRUE to center on page
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272 centered = TRUE,
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273 # optional caption
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274 caption = NULL,
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275 # h(inline); b(bottom); t (top) or p (separate page)
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276 anchor = "h",
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277 # set underscore_whack to TRUE to escape underscores
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278 underscore_whack = TRUE
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279 ) {
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280 if (is.null(justification))
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281 justification <-
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282 Reduce(
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283 f = paste,
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284 x = rep_len(if (right) "r" else "l", length(colnames(x)))
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285 )
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286 n <- length(rownames(x))
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287 if (length(x) == 0L) {
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288 cat(
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289 sprintf(
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290 # if n is one, use singular 'row', else use plural 'rows'
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291 ngettext(
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292 n,
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293 "data frame with 0 columns and %d row",
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294 "data frame with 0 columns and %d rows"
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295 ),
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296 n
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297 ),
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298 "\n",
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299 sep = ""
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300 )
22
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301 } else if (n == 0L) {
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302 cat("0 rows for:\n")
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303 latex_itemized_list(
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304 v = names(x),
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305 underscore_whack = underscore_whack
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306 )
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307 } else {
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308 if (is.null(max))
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309 max <- getOption("max.print", 99999L)
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310 if (!is.finite(max))
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311 stop("invalid 'max' / getOption(\"max.print\"): ",
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312 max)
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313 omit <- (n0 <- max %/% length(x)) < n
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314 m <- as.matrix(
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315 format.data.frame(
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316 if (omit) x[seq_len(n0), , drop = FALSE] else x,
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317 digits = digits,
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318 na.encode = FALSE
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319 )
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320 )
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321 cat(
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322 # h(inline); b(bottom); t (top) or p (separate page)
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323 paste0("\\begin{table}[", anchor, "]\n")
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324 )
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325 if (!is.null(caption))
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326 cat(paste0(" \\caption{", caption, "}"))
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327 if (centered) cat("\\centering\n")
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328 cat(
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329 paste(
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330 " \\begin{tabular}{",
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diff changeset
331 justification,
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diff changeset
332 "}\n",
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333 sep = ""
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334 )
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335 )
22
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336 # ref: https://tex.stackexchange.com/a/50353
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337 # Describes use of \rule{0pt}{3ex}
13
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338 if (!is.null(caption))
22
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339 cat("\\B \\\\ \\hline\\hline\n")
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diff changeset
340 # ref for top and bottom struts: https://tex.stackexchange.com/a/50355
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341 latex_table_row(
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342 v = colnames(m),
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343 extra = "\\T\\B",
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344 underscore_whack = underscore_whack
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345 )
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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346 cat("\\hline\n")
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347 for (i in seq_len(length(m[, 1]))) {
22
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348 latex_table_row(
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349 v = m[i, ],
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350 underscore_whack = underscore_whack
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diff changeset
351 )
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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352 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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353 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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354 paste(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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355 " \\end{tabular}",
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356 "\\end{table}",
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357 sep = "\n"
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358 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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359 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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360 if (omit)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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361 cat(" [ reached 'max' / getOption(\"max.print\") -- omitted",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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362 n - n0, "rows ]\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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363 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
364 invisible(x)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
365 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
366
22
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367 hypersub <-
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368 function(s) {
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369 hyper <- tolower(s)
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370 hyper <- gsub("[^a-z0-9]+", "-", hyper)
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371 hyper <- gsub("[-]+", "-", hyper)
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372 hyper <- sub("^[-]", "", hyper)
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373 hyper <- sub("[-]$", "", hyper)
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diff changeset
374 return(hyper)
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375 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
376
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377 subsection_header <-
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diff changeset
378 function(s) {
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379 hyper <- hypersub(s)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
380 cat(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
381 sprintf(
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382 "\\hypertarget{%s}\n{\\subsection{%s}\\label{%s}}\n",
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diff changeset
383 hyper, s, hyper
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diff changeset
384 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
385 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
386 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
387
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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388 subsubsection_header <-
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diff changeset
389 function(s) {
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390 hyper <- hypersub(s)
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diff changeset
391 cat(
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diff changeset
392 sprintf(
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393 "\\hypertarget{%s}\n{\\subsubsection{%s}\\label{%s}}\n",
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diff changeset
394 hyper, s, hyper
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diff changeset
395 )
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diff changeset
396 )
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diff changeset
397 }
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diff changeset
398
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
399 ### SQLite functions
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diff changeset
400
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
401 ddl_exec <- function(db, sql) {
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402 discard <- DBI::dbExecute(conn = db, statement = sql)
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diff changeset
403 if (FALSE && discard != 0) {
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diff changeset
404 need_newpage <- TRUE
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diff changeset
405 if (need_newpage) {
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406 need_newpage <<- FALSE
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diff changeset
407 cat("\\newpage\n")
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diff changeset
408 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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409 o_file <- stdout()
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diff changeset
410 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
411 cat(sql, file = o_file)
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412 cat(sprintf("\n%d rows affected by DDL\n", discard), file = o_file)
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diff changeset
413 cat("\n\\end{verbatim}\n")
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diff changeset
414 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
415 }
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diff changeset
416
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diff changeset
417 dml_no_rows_exec <- function(db, sql) {
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418 discard <- DBI::dbExecute(conn = db, statement = sql)
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diff changeset
419 if (discard != 0) {
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diff changeset
420 need_newpage <- TRUE
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421 if (need_newpage) {
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diff changeset
422 need_newpage <<- FALSE
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diff changeset
423 cat("\\newpage\n")
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diff changeset
424 }
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diff changeset
425 cat("\n\\begin{verbatim}\n")
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diff changeset
426 o_file <- stdout()
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diff changeset
427 cat(sql, file = o_file)
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428 cat(sprintf("\n%d rows affected by DML\n", discard), file = o_file)
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429 cat("\n\\end{verbatim}\n")
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430 }
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431 }
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432
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433 ### KSEA functions and helpers
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434
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435 # Adapted from KSEAapp::KSEA.Scores to allow retrieval of:
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436 # - maximum log2(FC)
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437 ksea_scores <- function(
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438
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439 # For human data, typically, ksdata = KSEAapp::ksdata
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440 ksdata,
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441
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442 # Input data file having columns:
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443 # - Protein : abbreviated protein name
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444 # - Gene : HUGO gene name
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445 # - Peptide : peptide sequence without indications of phosphorylation
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446 # - Reside.Both : position(s) of phosphorylation within Gene sequence
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447 # - First letter designates AA that is modified
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448 # - Numbers indicate position within Gene
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449 # - Multiple values are separated by semicolons
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450 # - p : p-value
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451 # - FC : fold-change
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452 px,
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453
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454 # A binary input of TRUE or FALSE, indicating whether or not to include
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455 # NetworKIN predictions
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456 networkin,
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457
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458 # A numeric value between 1 and infinity setting the minimum NetworKIN
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459 # score (can be left out if networkin = FALSE)
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460 networkin_cutoff
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461
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462 ) {
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463 if (length(grep(";", px$Residue.Both)) == 0) {
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464 # There are no Residue.Both entries having semicolons, so new is
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465 # simply px except two columns are renamed and a column is added
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466 # for log2(abs(fold-change))
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467 new <- px
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468 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD")
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469 new$log2_fc <- log2(abs(as.numeric(as.character(new$FC))))
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470 new <- new[complete.cases(new$log2_fc), ]
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471 } else {
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472 # Split each row having semicolons in Residue.Both into rows that are
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473 # duplicated in all respects except that each row has a single
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474 # member of the set "split-on-semicolon-Residue.Both"
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475 px_double <- px[grep(";", px$Residue.Both), ]
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476 residues <- as.character(px_double$Residue.Both)
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477 residues <- as.matrix(residues, ncol = 1)
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478 split <- strsplit(residues, split = ";")
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479 # x gets count of residues in each row,
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480 # i.e., 1 + count of semicolons
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481 x <- sapply(split, length)
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482 # Here is the set of split rows
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483 px_single <- data.frame(
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484 Protein = rep(px_double$Protein, x),
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485 Gene = rep(px_double$Gene, x),
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486 Peptide = rep(px_double$Peptide, x),
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487 Residue.Both = unlist(split),
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488 p = rep(px_double$p, x),
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489 FC = rep(px_double$FC, x)
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490 )
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491 # new first gets the split rows
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492 new <- px[-grep(";", px$Residue.Both), ]
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493 # to new, append the rows that didn't need splitting in the first place
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494 new <- rbind(new, px_single)
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495 # map Gene to SUB_GENE
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496 # map Residue.Both to SUB_MOD_RSD
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497 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD")
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498 # Eliminate any non-positive values to prevent introduction of
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499 # infinite or NaN values
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500 new[(0 <= new$log2_fc), "log2_fc"] <- NA
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501 # Because of preceding step, there is no need for abs in the next line
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502 new$log2_fc <- log2(as.numeric(as.character(new$FC)))
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503 # Convert any illegal values from NaN to NA
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504 new[is.nan(new$log2_fc), "log2_fc"] <- NA
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505 # Eliminate rows having missing values (e.g., non-imputed data)
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506 new <- new[complete.cases(new$log2_fc), ]
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507 }
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508 if (networkin == TRUE) {
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509 # When NetworKIN is true, filter on NetworKIN.cutoff which includes
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510 # PhosphoSitePlus data *because its networkin_score is set to Inf*
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511 ksdata_filtered <- ksdata[grep("[a-z]", ksdata$Source), ]
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512 ksdata_filtered <- ksdata_filtered[
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513 (ksdata_filtered$networkin_score >= networkin_cutoff), ]
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514 } else {
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515 # Otherwise, simply use PhosphSitePlus rows
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516 ksdata_filtered <- ksdata[
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517 grep("PhosphoSitePlus", ksdata$Source), ]
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518 }
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519 # Join the two data.frames on common columns SUB_GENE and SUB_MOD_RSD
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520 # colnames of ksdata_filtered:
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521 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE" "SUB_GENE_ID"
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522 # "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD" "SITE_GRP_ID"
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523 # "SITE_...7_AA" "networkin_score" "Source"
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524 # colnames of new:
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525 # "Protein" "SUB_GENE" "Peptide" "SUB_MOD_RSD" "p" "FC" "log2_fc"
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526 # Equivalent to:
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527 # SELECT a.*. b.Protein, b.Peptide, b.p, b.FC, b.log2_fc
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528 # FROM ksdata_filtered a
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529 # INNER JOIN new b
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530 # ON a.SUB_GENE = b.SUB_GENE
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531 # AND a.SUB_MOD_RSD = b.SUB_MOD_RSD
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532 ksdata_dataset <- base::merge(ksdata_filtered, new)
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533 # colnames of ksdata_dataset:
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534 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE"
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535 # "SUB_GENE_ID" "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD"
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536 # "SITE_GRP_ID" "SITE_...7_AA" "networkin_score" "Source" "Protein"
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537 # "Peptide" "p" "FC" "log2_fc" (uniprot_no_isoform)
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538 # Re-order dataset; prior to accounting for isoforms
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539 ksdata_dataset <- ksdata_dataset[order(ksdata_dataset$GENE), ]
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540 # Extract non-isoform accession in UniProtKB
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541 ksdata_dataset$uniprot_no_isoform <- sapply(
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542 ksdata_dataset$KIN_ACC_ID,
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543 function(x) unlist(strsplit(as.character(x), split = "-"))[1]
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544 )
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545 # Discard previous results while selecting interesting columns ...
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546 ksdata_dataset_abbrev <- ksdata_dataset[, c(5, 1, 2, 16:19, 14)]
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547 # Column names are now:
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548 # "GENE" "SUB_GENE" "SUB_MOD_RSD" "Peptide" "p"
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549 # "FC" "log2_fc" "Source"
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550 # Make column names human-readable
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551 colnames(ksdata_dataset_abbrev) <- c(
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552 "Kinase.Gene", "Substrate.Gene", "Substrate.Mod", "Peptide", "p",
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553 "FC", "log2FC", "Source"
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554 )
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555 # SELECT * FROM ksdata_dataset_abbrev
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556 # ORDER BY Kinase.Gene, Substrate.Gene, Substrate.Mod, p
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557 ksdata_dataset_abbrev <-
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558 ksdata_dataset_abbrev[
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559 order(
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560 ksdata_dataset_abbrev$Kinase.Gene,
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561 ksdata_dataset_abbrev$Substrate.Gene,
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562 ksdata_dataset_abbrev$Substrate.Mod,
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563 ksdata_dataset_abbrev$p),
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564 ]
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565 # First aggregation step to account for multiply phosphorylated peptides
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566 # and differing peptide sequences; the goal here is to combine results
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567 # for all measurements of the same substrate.
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568 # SELECT `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`,
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569 # `Source`, avg(log2FC) AS log2FC
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570 # FROM ksdata_dataset_abbrev
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571 # GROUP BY `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`,
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572 # `Source`
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573 # ORDER BY `Kinase.Gene`;
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574 # in two steps:
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575 # (1) compute average log_2(fold-change)
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576 ksdata_dataset_abbrev <- aggregate(
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577 log2FC ~ Kinase.Gene + Substrate.Gene + Substrate.Mod + Source,
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578 data = ksdata_dataset_abbrev,
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579 FUN = mean
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580 )
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581 # (2) order by Kinase.Gene
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582 ksdata_dataset_abbrev <-
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583 ksdata_dataset_abbrev[order(ksdata_dataset_abbrev$Kinase.Gene), ]
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584 # SELECT `Kinase.Gene`, count(*)
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585 # FROM ksdata_dataset_abbrev
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586 # GROUP BY `Kinase.Gene`;
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587 # in two steps:
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588 # (1) Extract the list of Kinase.Gene names
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589 kinase_list <- as.vector(ksdata_dataset_abbrev$Kinase.Gene)
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590 # (2) Convert to a named list of counts of kinases in ksdata_dataset_abrev,
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591 # named by Kinase.Gene
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592 kinase_list <- as.matrix(table(kinase_list))
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593 # Second aggregation step to account for all substrates per kinase
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594 # CREATE TABLE mean_fc
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595 # AS
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596 # SELECT `Kinase.Gene`, avg(log2FC) AS log2FC
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597 # FROM ksdata_dataset_abbrev
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598 # GROUP BY `Kinase.Gene`
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599 mean_fc <- aggregate(
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600 log2FC ~ Kinase.Gene,
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601 data = ksdata_dataset_abbrev,
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602 FUN = mean
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603 )
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604 # mean_fc columns: "Kinase.Gene", "log2FC"
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605 if (FALSE) {
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606 # I need to re-think this; I was trying to find the most-represented
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607 # peptide, but that horse has already left the barn
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608 # SELECT `Kinase.Gene`, max(abs(log2FC)) AS log2FC
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609 # FROM ksdata_dataset_abbrev
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610 # GROUP BY `Kinase.Gene`
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611 max_fc <- aggregate(
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612 log2FC ~ Kinase.Gene,
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613 data = ksdata_dataset_abbrev,
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614 FUN = function(r) max(abs(r))
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615 )
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616 }
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617
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618 # Create column 3: mS
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619 mean_fc$m_s <- mean_fc[, 2]
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620 # Create column 4: Enrichment
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621 mean_fc$enrichment <- mean_fc$m_s / abs(mean(new$log2_fc, na.rm = TRUE))
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622 # Create column 5: m, count of substrates
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623 mean_fc$m <- kinase_list
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624 # Create column 6: z-score
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625 mean_fc$z_score <- (
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626 (mean_fc$m_s - mean(new$log2_fc, na.rm = TRUE)) *
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627 sqrt(mean_fc$m)) / sd(new$log2_fc, na.rm = TRUE)
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628 # Create column 7: p-value, deduced from z-score
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629 mean_fc$p_value <- pnorm(-abs(mean_fc$z_score))
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630 # Create column 8: FDR, deduced by Benjamini-Hochberg adustment from p-value
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631 mean_fc$fdr <- p.adjust(mean_fc$p_value, method = "fdr")
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632
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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633 # Remove log2FC column, which is duplicated as mS
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634 mean_fc <- mean_fc[order(mean_fc$Kinase.Gene), -2]
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635 # Correct the column names which we had to hack because of the linter...
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636 colnames(mean_fc) <- c(
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637 "Kinase.Gene", "mS", "Enrichment", "m", "z.score", "p.value", "FDR"
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diff changeset
638 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
639 return(mean_fc)
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diff changeset
640 }
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diff changeset
641
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
642 low_fdr_barplot <- function(
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diff changeset
643 rslt,
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diff changeset
644 i_cntrst,
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diff changeset
645 i,
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diff changeset
646 a_level,
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diff changeset
647 b_level,
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diff changeset
648 fold_change,
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diff changeset
649 caption
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diff changeset
650 ) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
651 rslt_score_list_i <- rslt$score_list[[i]]
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652 if (!is.null(rslt_score_list_i)) {
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653 rslt_score_list_i_nrow <- nrow(rslt_score_list_i)
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diff changeset
654 k <- data.frame(
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655 contrast = as.integer(i_cntrst),
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656 a_level = rep.int(a_level, rslt_score_list_i_nrow),
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657 b_level = rep.int(b_level, rslt_score_list_i_nrow),
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658 kinase_gene = rslt_score_list_i$Kinase.Gene,
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659 mean_log2_fc = rslt_score_list_i$mS,
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660 enrichment = rslt_score_list_i$Enrichment,
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661 substrate_count = rslt_score_list_i$m,
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662 z_score = rslt_score_list_i$z.score,
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663 p_value = rslt_score_list_i$p.value,
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664 fdr = rslt_score_list_i$FDR
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665 )
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diff changeset
666 selector <- switch(
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diff changeset
667 ksea_cutoff_statistic,
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668 "FDR" = {
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diff changeset
669 k$fdr
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670 },
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diff changeset
671 "p.value" = {
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diff changeset
672 k$p_value
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diff changeset
673 },
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
674 stop(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
675 sprintf(
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676 "Unexpected cutoff statistic %s rather than 'FDR' or '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
677 ksea_cutoff_statistic
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678 )
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diff changeset
679 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
680 )
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diff changeset
681
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
682 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
683
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
684 if (nrow(k) > 0) {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
685 op <- par(mai = c(1, 1.5, 0.4, 0.4))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
686 numeric_z_score <- as.numeric(k$z_score)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
687 z_score_order <- order(numeric_z_score)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
688 kinase_name <- k$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
689 long_caption <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
690 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
691 "Kinase z-score, %s < %s, %s",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
692 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
693 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
694 caption
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
695 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
696 my_cex_caption <- 65.0 / max(65.0, nchar(long_caption))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
697 cat("\n\\clearpage\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
698 barplot(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
699 height = numeric_z_score[z_score_order],
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
700 border = NA,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
701 xpd = FALSE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
702 cex.names = 1.0,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
703 main = long_caption,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
704 cex.main = my_cex_caption,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
705 names.arg = kinase_name[z_score_order],
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
706 horiz = TRUE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
707 srt = 45,
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
708 las = 1,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
709 cex.axis = 0.9
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
710 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
711 par(op)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
712 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
713 }
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
714 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
715
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
716 # 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
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parents: 15
diff changeset
717
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
718 low_fdr_print <- function(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
719 rslt,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
720 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
721 i,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
722 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
723 b_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
724 fold_change,
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
725 caption
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
726 ) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
727 rslt_score_list_i <- rslt$score_list[[i]]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
728 if (!is.null(rslt_score_list_i)) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
729 rslt_score_list_i_nrow <- nrow(rslt_score_list_i)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
730 k <- contrast_ksea_scores <- data.frame(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
731 contrast = as.integer(i_cntrst),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
732 a_level = rep.int(a_level, rslt_score_list_i_nrow),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
733 b_level = rep.int(b_level, rslt_score_list_i_nrow),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
734 kinase_gene = rslt_score_list_i$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
735 mean_log2_fc = rslt_score_list_i$mS,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
736 enrichment = rslt_score_list_i$Enrichment,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
737 substrate_count = rslt_score_list_i$m,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
738 z_score = rslt_score_list_i$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
739 p_value = rslt_score_list_i$p.value,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
740 fdr = rslt_score_list_i$FDR
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
741 )
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
742
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
743 selector <- switch(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
744 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
745 "FDR" = {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
746 k$fdr
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
747 },
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
748 "p.value" = {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
749 k$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
750 },
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
751 stop(
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
752 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
753 "Unexpected cutoff statistic %s rather than 'FDR' or '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
754 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
755 )
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
756 )
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
757 )
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
758
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
759 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
760 # 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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diff changeset
761 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
762 ksea_asterisk_hash[[kinase_name]] <- 1
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
763 }
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
764
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
765 db_write_table_overwrite <- (i_cntrst < 2)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
766 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
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diff changeset
767 RSQLite::dbWriteTable(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
768 conn = db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
769 name = "contrast_ksea_scores",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
770 value = contrast_ksea_scores,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
771 append = db_write_table_append
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
772 )
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
773 selector <- switch(
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
774 ksea_cutoff_statistic,
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
775 "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
776 contrast_ksea_scores$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
777 },
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
778 "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
779 contrast_ksea_scores$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
780 },
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
781 stop(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
782 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
783 "Unexpected cutoff statistic %s rather than 'FDR' or '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
784 ksea_cutoff_statistic
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
785 )
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
786 )
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
787 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
788 output_df <- contrast_ksea_scores[
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
789 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
790 c("kinase_gene", "mean_log2_fc", "enrichment", "substrate_count",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
791 "z_score", "p_value", "fdr")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
792 ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
793 output_order <- with(output_df, order(mean_log2_fc, 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
794 output_df <- output_df[output_order, ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
795 colnames(output_df) <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
796 c(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
797 colnames(output_df)[1],
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
798 colnames(output_df)[2],
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
799 "enrichment",
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
800 "m_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
801 "z_score",
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
802 "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
803 "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
804 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
805 output_df$fdr <- sprintf("%0.4f", output_df$fdr)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
806 output_df$p_value <- sprintf("%0.2e", output_df$p_value)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
807 output_df$z_score <- sprintf("%0.2f", output_df$z_score)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
808 output_df$m_s <- sprintf("%d", output_df$m_s)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
809 output_df$enrichment <- sprintf("%0.2f", output_df$enrichment)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
810 output_ncol <- ncol(output_df)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
811 colnames(output_df) <-
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
812 c(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
813 "Kinase",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
814 "\\(\\overline{\\log_2 (|\\text{fold-change}|)}\\)",
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
815 "Enrichment",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
816 "Substrates",
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
817 "z-score",
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
818 "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
819 "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
820 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
821 selector <- switch(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
822 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
823 "FDR" = {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
824 rslt$score_list[[i]]$FDR
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
825 },
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
826 "p.value" = {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
827 rslt$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
828 },
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
829 stop(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
830 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
831 "Unexpected cutoff statistic %s rather than 'FDR' or '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
832 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
833 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
834 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
835 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
836 if (sum(selector < ksea_cutoff_threshold) > 0) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
837 math_caption <- gsub("{", "\\{", caption, fixed = TRUE)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
838 math_caption <- gsub("}", "\\}", math_caption, fixed = TRUE)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
839 data_frame_latex(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
840 x = output_df,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
841 justification = "l c c c c c c",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
842 centered = TRUE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
843 caption = sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
844 "\\text{%s}, %s < %s",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
845 math_caption,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
846 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
847 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
848 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
849 anchor = const_table_anchor_p
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
850 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
851 } else {
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
852 cat(
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
853 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
854 "\\break
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
855 No kinases had
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
856 \\(\\text{%s}_\\text{enrichment} < %s\\)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
857 for contrast %s\\hfill\\break\n",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
858 ksea_cutoff_statistic,
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
859 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
860 caption
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
861 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
862 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
863 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
864 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
865 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
866
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
867 # 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
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diff changeset
868 create_breaks <- function(merged_scores) {
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
869 if (sum(!is.na(merged_scores)) < 2)
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
870 return(NULL)
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
871 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
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diff changeset
872 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
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parents: 15
diff changeset
873 breaks_neg <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
874 append(
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
875 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
876 breaks_neg
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
877 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
878 breaks_neg <- sort(unique(breaks_neg))
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
879 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
880 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
881 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
882 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
883 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
884 breaks_pos <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
885 append(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
886 breaks_pos,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
887 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
888 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
889 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
890 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
891 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
892 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
893 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
894 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
895 mycol_neg <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
896 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
897 low = "blue",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
898 high = "white")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
899 mycol_pos <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
900 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
901 low = "white",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
902 high = "red")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
903 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
904 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
905 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
906 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
907
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
908 # 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
909 draw_kseaapp_summary_heatmap <- function(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
910 x,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
911 sample_cluster,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
912 merged_asterisk,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
913 my_cex_row,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
914 color_breaks,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
915 margins,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
916 ...
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
917 ) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
918 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
919 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
920 cat(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
921 paste0(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
922 "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
923 typeof(x),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
924 "' 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
925 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
926 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
927 } else if (nrow(x) < 2) {
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
928 cat("No plot because matrix has ", nrow(x), " rows.\n\n")
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
929 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
930 } else if (ncol(x) < 2) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
931 cat("No plot because matrix x has ", ncol(x), " columns.\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
932 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
933 } else {
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
934 my_limit <- 25
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
935 my_cex_col <- my_limit / (my_limit + ncol(x))
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
936 my_cex_row <- my_limit / (my_limit + nrow(x))
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
937 my_scale <- 12.0
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
938 if (ncol(x) < 10 && nrow(x) < 10)
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
939 my_scale <- my_scale * 10 / (10 - nrow(x)) * 10 / (10 - ncol(x))
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
940 gplots::heatmap.2(
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
941 x = merged_scores,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
942 Colv = sample_cluster,
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
943 breaks = color_breaks[[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
944 cellnote = merged_asterisk,
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
945 cexCol = 0.9 * my_cex_col,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
946 cexRow = 2 * my_cex_row,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
947 col = color_breaks[[2]],
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
948 density.info = "none",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
949 key = FALSE,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
950 lhei = c(0.4, 8.0, 1.1),
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
951 lmat = rbind(c(0, 3), c(2, 1), c(0, 4)),
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
952 lwid = c(0.5, 3),
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
953 margins = margins,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
954 notecex = my_scale * my_cex_row * my_cex_col,
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
955 notecol = "white",
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
956 scale = "none",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
957 srtCol = 45,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
958 srtRow = 45,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
959 trace = "none",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
960 ...
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
961 )
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
962 return(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
963 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
964 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
965
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
966 # Adapted from KSEAapp::KSEA.Heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
967 ksea_heatmap <- function(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
968 # 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
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diff changeset
969 score_list,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
970 # 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
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diff changeset
971 # - 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
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diff changeset
972 # - 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
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diff changeset
973 sample_labels,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
974 # 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
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diff changeset
975 # to use for marking statistically significant scores
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
976 stats,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
977 # 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
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diff changeset
978 # 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
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diff changeset
979 m_cutoff,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
980 # 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
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diff changeset
981 # for indicating significant kinases in 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
982 p_cutoff =
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
983 stop("argument 'p_cutoff' is required for function 'ksea_heatmap'"),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
984 # 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
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diff changeset
985 # hierarchical clustering of the sample columns
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
986 sample_cluster,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
987 # 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
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diff changeset
988 # 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
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diff changeset
989 export = FALSE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
990 # bottom and right margins; adjust as needed if contrast names are too long
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
991 margins = c(6, 20),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
992 # print which kinases?
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
993 # - 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
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diff changeset
994 which_kinases,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
995 # 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
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diff changeset
996 # - main: main title of plot
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
997 # - xlab: x-axis label
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
998 # - ylab: y-axis label
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
999 ...
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1000 ) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1001 filter_m <- function(dataset, m_cutoff) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1002 filtered <- dataset[(dataset$m >= m_cutoff), ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1003 return(filtered)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1004 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1005 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
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diff changeset
1006 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
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diff changeset
1007 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
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diff changeset
1008 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
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diff changeset
1009 paste(names, i, sep = ".")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1010 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1011 master <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1012 Reduce(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1013 f = function(...) {
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1014 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
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diff changeset
1015 },
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1016 x = score_list_m
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1017 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1018
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1019 row.names(master) <- master$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
1020 columns <- as.character(colnames(master))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1021 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
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diff changeset
1022 colnames(merged_scores) <- sample_labels
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1023 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
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diff changeset
1024 asterisk <- function(mtrx, p_cutoff) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1025 new <- 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
1026 for (i in seq_len(nrow(mtrx))) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1027 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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diff changeset
1028 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
1029 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
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parents: 15
diff changeset
1030 new[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
1031 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1032 new[i, j] <- ""
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1033 }
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
1034 }
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
1035 }
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
1036 return(new)
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
1037 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1038 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
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diff changeset
1039
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1040 # begin hack to print only significant rows
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1041 asterisk_rows <- rowSums(merged_asterisk == "*") > 0
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1042 all_rows <- rownames(merged_stats)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1043 names(asterisk_rows) <- all_rows
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1044 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
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diff changeset
1045 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
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diff changeset
1046 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
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diff changeset
1047 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
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diff changeset
1048 # end hack to print only significant rows
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1049
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1050 row_list <- list()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1051 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
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diff changeset
1052 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
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diff changeset
1053 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
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diff changeset
1054
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1055 i <- which_kinases
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1056 my_row_names <- row_list[[i]]
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1057 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
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diff changeset
1058 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
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diff changeset
1059 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
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diff changeset
1060
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1061 color_breaks <- create_breaks(scrs)
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1062 if (is.null(color_breaks)) {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1063 cat("No plot because matrix has too many missing values.\n\n")
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1064 return(NULL)
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1065 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1066 plot_height <- nrow(scrs) ^ 0.55
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1067 plot_width <- ncol(scrs) ^ 0.7
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1068 my_cex_row <- 0.25 * 16 / plot_height
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1069 if (export == "TRUE") {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1070 png(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1071 "KSEA.Merged.Heatmap.png",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1072 width = plot_width * 300,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1073 height = 2 * plot_height * 300,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1074 res = 300,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1075 pointsize = 14
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1076 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1077 }
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1078 did_draw <- draw_kseaapp_summary_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
1079 x = scrs,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1080 sample_cluster = sample_cluster,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1081 merged_asterisk = merged_asterisk,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1082 my_cex_row = my_cex_row,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1083 color_breaks = color_breaks,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1084 margins = margins
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1085 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1086 if (export == "TRUE") {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1087 dev.off()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1088 }
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1089 if (!did_draw)
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1090 return(NULL)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1091 return(my_row_names)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1092 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1093
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1094 # helper for heatmaps of phosphopeptide intensities
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1095
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1096 draw_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
1097 function(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1098 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
1099 cutoff, # cutoff used by hm_heading_function
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1100 hm_heading_function, # construct and cat heading from m and cutoff
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1101 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
1102 suppress_row_dendrogram = TRUE, # set to false to show dendrogram
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1103 max_peptide_count # experimental:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1104 = intensity_hm_rows, # values of 50 and 75 worked well
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1105 ... # passthru parameters 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
1106 ) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1107 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
1108 # 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
1109 if (hm_heading_function(m, cutoff)) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1110 peptide_count <- min(max_peptide_count, nrow(m))
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1111 if (nrow(m) > 0) {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1112 m_margin <- m[peptide_count:1, ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1113 # Margin setting was heuristically derived
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1114 margins <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1115 c(0.5, # col
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1116 max(80, sqrt(nchar(rownames(m_margin)))) * 5 / 16 # row
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1117 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1118 }
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1119 if (nrow(m) > 0) {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1120 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
1121 tryCatch(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1122 {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1123 old_oma <- par("oma")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1124 par(cex.main = 0.6)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1125 # Heuristically determined character size adjustment formula
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1126 my_cex_row <-
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1127 250000 / (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1128 max(4500, (nchar(rownames(m_margin)))^2) * intensity_hm_rows
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1129 )
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1130 m_hm <- m[peptide_count:1, , drop = FALSE]
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1131 my_limit <- 60
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1132 my_cex_col <- 0.75 * my_limit / (my_limit + ncol(m_hm))
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
1133 hm_call <- function(x, scaling, title) {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1134 heatmap(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1135 x,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1136 Rowv = if (suppress_row_dendrogram) NA else NULL,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1137 Colv = NA,
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
1138 cexRow = my_cex_row,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1139 cexCol = my_cex_col,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1140 scale = scaling,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1141 margins = margins,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1142 main = title,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1143 xlab = "",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1144 las = 1,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1145 ...
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1146 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1147 }
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1148 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
1149 hm_call(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1150 m_hm,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1151 "none",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1152 "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
1153 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1154 else
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1155 hm_call(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1156 m_hm,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1157 "row",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1158 "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
1159 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1160 },
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1161 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
1162 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
1163 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
1164 tryCatch(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1165 {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1166 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
1167 hm_call(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1168 m_hm,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1169 "none",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1170 paste(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1171 "log(intensities), unscaled, unimputed,",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1172 "NAs zeroed, unnormalized"
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1173 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1174 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1175 else
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1176 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
1177 },
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1178 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
1179 cat(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1180 sprintf(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1181 "\n%s %s Internal message: %s\n",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1182 "Could not draw heatmap,",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1183 "possibly because of too many missing values.",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1184 r$message
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1185 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1186 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1187 }
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1188 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1189 } else {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1190 cat(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1191 "\nCould not draw 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
1192 )
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1193 }
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1194 },
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1195 finally = par(old_oma)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1196 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1197 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1198 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1199 return(peptide_count)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1200 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1201 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1202
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1203 ```{r, 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
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diff changeset
1204 cat("\\listoftables\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1205 ```
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1206 # 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
1207
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1208 To perform for phosphopeptides:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1209
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1210 - imputation of missing values,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1211 - quantile normalization,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1212 - ANOVA (using the R stats::`r params$oneWayManyCategories` function), and
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1213 - 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
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diff changeset
1214 - 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
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diff changeset
1215 - 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
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diff changeset
1216 - NetworKIN [http://networkin.science/](http://networkin.science/)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1217 - 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"
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parents:
diff changeset
1218
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1219 ```{r include = 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
1220
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1221 ### GLOBAL VARIABLES
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1222
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1223 # parameters for KSEA
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1224
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1225 ksea_cutoff_statistic <- params$kseaCutoffStatistic
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1226 ksea_cutoff_threshold <- params$kseaCutoffThreshold
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1227 ksea_min_kinase_count <- params$kseaMinKinaseCount
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
1228
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1229 ksea_heatmap_titles <- list()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1230 ksea_heatmap_titles[[const_ksea_astrsk_kinases]] <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1231 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1232 "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
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diff changeset
1233 ksea_cutoff_statistic,
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
1234 ksea_cutoff_threshold
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
1235 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1236 ksea_heatmap_titles[[const_ksea_all_kinases]] <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1237 "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
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diff changeset
1238 ksea_heatmap_titles[[const_ksea_nonastrsk_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
1239 sprintf(
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
1240 "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
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parents: 15
diff changeset
1241 ksea_cutoff_statistic,
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
1242 ksea_cutoff_threshold
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
1243 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1244 # 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
1245 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
1246
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
1247 # READ PARAMETERS (mostly)
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
1248
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1249 intensity_hm_rows <- params$intensityHeatmapRows
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
1250 # Input Filename
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1251 input_file <- params$inputFile
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1252
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
1253 # First data column - ideally, this could be detected via regexSampleNames,
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
1254 # but for now leave it as is.
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1255 first_data_column <- params$firstDataColumn
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1256 fdc_is_integer <- is.integer(first_data_column)
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1257 if (fdc_is_integer) {
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
1258 first_data_column <- as.integer(params$firstDataColumn)
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
1259 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1260
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
1261 # 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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parents: 0
diff changeset
1262 # Since pY abundance is low, set to 0.10 and 0.20 in addition to 0.05
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
1263 val_fdr <-
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
1264 read.table(file = params$alphaFile, sep = "\t", header = FALSE, quote = "")
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1265
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1266 if (
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
1267 ncol(val_fdr) != 1 ||
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
1268 sum(!is.numeric(val_fdr[, 1])) ||
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
1269 sum(val_fdr[, 1] < 0) ||
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1270 sum(val_fdr[, 1] > 1)
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
1271 ) {
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
1272 stop("alphaFile should be one column of numbers within the range [0.0,1.0]")
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1273 }
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
1274 val_fdr <- val_fdr[, 1]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1275
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1276 #Imputed Data filename
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1277 imputed_data_filename <- params$imputedDataFilename
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
1278 imp_qn_lt_data_filenm <- params$imputedQNLTDataFile
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1279 anova_ksea_mtdt_file <- params$anovaKseaMetadata
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1280
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
1281 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1282
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1283 ```{r echo = FALSE}
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1284 # Imputation method, should be one of
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1285 # "random", "group-median", "median", or "mean"
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1286 imputation_method <- params$imputationMethod
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1287
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1288 # Selection of percentile of logvalue data to set the mean for random number
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
1289 # generation when using random imputation
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1290 mean_percentile <- params$meanPercentile / 100.0
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1291
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1292 # deviation adjustment-factor for random values; real number.
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1293 sd_percentile <- params$sdPercentile
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1294
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
1295 # Regular expression of Sample Names, e.g., "\\.(\\d+)[A-Z]$"
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1296 regex_sample_names <- params$regexSampleNames
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1297
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1298 # Regular expression to extract Sample Grouping from Sample Name;
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1299 # if error occurs, compare sample_treatment_levels vs. sample_name_matches
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1300 # to see if groupings/pairs line up
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1301 # e.g., "(\\d+)"
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1302 regex_sample_grouping <- params$regexSampleGrouping
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1303
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1304 one_way_all_categories_fname <- params$oneWayManyCategories
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1305 one_way_all_categories <- try_catch_w_e(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1306 match.fun(one_way_all_categories_fname))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1307 if (!is.function(one_way_all_categories$value)) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1308 write("fatal error for parameter oneWayManyCategories:", stderr())
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1309 write(one_way_all_categories$value$message, stderr())
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1310 if (sys.nframe() > 0) quit(save = "no", status = 1)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1311 stop("Cannot continue. Goodbye.")
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
1312 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1313 one_way_all_categories <- one_way_all_categories$value
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1314
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1315 one_way_two_categories_fname <- params$oneWayManyCategories
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1316 one_way_two_categories <- try_catch_w_e(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1317 match.fun(one_way_two_categories_fname))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1318 if (!is.function(one_way_two_categories$value)) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1319 cat("fatal error for parameter oneWayTwoCategories: \n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1320 cat(one_way_two_categories$value$message, fill = TRUE)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1321 if (sys.nframe() > 0) quit(save = "no", status = 1)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1322 stop("Cannot continue. Goodbye.")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1323 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1324 one_way_two_categories <- one_way_two_categories$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
1325
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1326 preproc_db <- params$preprocDb
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1327 ksea_app_prep_db <- params$kseaAppPrepDb
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1328 result <- file.copy(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1329 from = preproc_db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1330 to = ksea_app_prep_db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1331 overwrite = TRUE
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
1332 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1333 if (!result) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1334 write(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1335 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1336 "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
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diff changeset
1337 preproc_db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1338 ksea_app_prep_db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1339 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1340 stderr()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1341 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1342 if (sys.nframe() > 0) quit(save = "no", status = 1)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1343 stop("Cannot continue. Goodbye.")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1344 }
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
1345 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1346
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
1347 ```{r echo = FALSE}
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1348 ### READ DATA
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
1349
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
1350 # 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"
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parents: 0
diff changeset
1351 # - 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"
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diff changeset
1352 full_data <- read.table(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1353 file = input_file,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1354 sep = "\t",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
1355 header = TRUE,
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1356 quote = "",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1357 check.names = FALSE
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1358 )
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
1359 ```
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1360
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1361 # Extract Sample Classes and Names
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1362
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
1363 Column names parsed from input file are shown in Table 1; sample classes and names, in Table 2.
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1364
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1365 ```{r echo = FALSE, results = 'asis'}
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diff changeset
1366
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
1367 data_column_indices <- grep(first_data_column, names(full_data), perl = TRUE)
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1368
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1369 if (!fdc_is_integer) {
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
1370 if (length(data_column_indices) > 0) {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
1371 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"
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parents:
diff changeset
1372 } else {
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
1373 stop(paste("failed to convert firstDataColumn:", first_data_column))
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
1374 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
1375 }
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
1376
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1377 cat(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1378 sprintf(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1379 paste(
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
1380 "\n\nThe input data file has peptide-intensity data for each sample",
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1381 "in one of columns %d through %d.\n\n"
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1382 ),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1383 min(data_column_indices),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1384 max(data_column_indices)
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1385 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1386 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1387
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1388 # Write column names as a LaTeX enumerated list.
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1389 column_name_df <- data.frame(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1390 column = seq_len(length(colnames(full_data))),
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
1391 name = paste0("\\verb@", colnames(full_data), "@")
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1392 )
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
1393 cat("\n\\begin{tiny}\n")
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1394 data_frame_latex(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1395 x = column_name_df,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1396 justification = "l l",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1397 centered = TRUE,
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 caption = "Input data column names",
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
1399 anchor = const_table_anchor_bp,
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
1400 underscore_whack = FALSE
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1401 )
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
1402 cat("\n\\end{tiny}\n")
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1403
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1404 ```
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
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
1406 ```{r echo = FALSE, results = 'asis'}
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
1407 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"
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parents: 12
diff changeset
1408 quant_data[quant_data == 0] <- NA
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
1409 rownames(quant_data) <- rownames(full_data) <- full_data$Phosphopeptide
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1410 # Extract factors and trt-replicates using regular expressions.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1411 # Typically:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
1412 # regex_sample_names is "\\.\\d+[A-Z]$"
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
1413 # regex_sample_grouping is "\\d+"
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
1414 # 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
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parents: 15
diff changeset
1415 # 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
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parents: 15
diff changeset
1416 # e.g.:
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
1417 # group .1A .1B .1C into group 1;
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
1418 # group .2A .2B .2C, into group 2;
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
1419 # etc.
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
1420 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"
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parents: 12
diff changeset
1421 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"
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parents: 12
diff changeset
1422 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
1423
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1424 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
1425
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1426 rx_match <- regexpr(regex_sample_grouping, sample_name_matches, perl = TRUE)
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
1427 sample_treatment_levels <- as.factor(regmatches(sample_name_matches, rx_match))
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
1428 number_of_samples <- length(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
1429 sample_treatment_df <- data.frame(
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
1430 class = sample_treatment_levels,
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
1431 sample = sample_name_matches
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
1432 )
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
1433 # reorder data
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
1434 if (TRUE) {
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
1435 my_order <- with(sample_treatment_df, order(class, sample))
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
1436 quant_data <- quant_data[, my_order]
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
1437 sample_name_matches <- sample_name_matches[my_order]
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
1438 sample_treatment_levels <- sample_treatment_levels[my_order]
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
1439 }
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
1440 sample_treatment_df <- data.frame(
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
1441 class = sample_treatment_levels,
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
1442 sample = sample_name_matches
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
1443 )
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
1444 data_frame_latex(
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
1445 x = sample_treatment_df,
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
1446 justification = "rp{0.2\\linewidth} lp{0.3\\linewidth}",
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
1447 centered = TRUE,
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
1448 caption = "Sample classes",
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
1449 anchor = const_table_anchor_tbp,
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
1450 underscore_whack = FALSE
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
1451 )
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
1452 sample_name_shrink <- 10 / (10 + max(nchar(sample_name_matches)))
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1453 ```
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1454
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1455 ```{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
1456 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
1457 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1458
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1459 ## 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
1460
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1461 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1462
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1463 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
1464 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
1465
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1466 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
1467 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
1468
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1469 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
1470
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1471 # data visualization
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1472 old_par <- par(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1473 mai = par("mai") + c(0.5, 0, 0, 0)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1474 )
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1475 # 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
1476 # Vertical plot
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1477 boxplot(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1478 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
1479 , las = 2
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1480 , cex.axis = 0.9 * sample_name_shrink
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1481 , 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
1482 , 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
1483 , xlab = "Sample"
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1484 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1485 par(old_par)
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1486
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1487
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1488
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1489 cat("\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
1490 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
1491
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1492 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1493
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1494 ```{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
1495 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
1496 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
1497 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
1498 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
1499 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
1500 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
1501 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1502 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
1503 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1504 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1505
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1506 ## 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
1507
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1508 <!--
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1509 # 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
1510 # 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
1511 # 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
1512 # 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
1513 # 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
1514 -->
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1515 ```{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
1516
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1517 # 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
1518 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
1519
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1520 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
1521 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
1522 plot(
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1523 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
1524 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
1525 "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
1526 ),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1527 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
1528 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
1529 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1530 hist(
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1531 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
1532 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
1533 breaks = 100,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1534 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
1535 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
1536 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1537 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1538
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1539 ## 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
1540
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1541 ```{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
1542 # determine quantile
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1543 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
1544
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1545 # 1 = row of matrix (ie, phosphopeptide)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1546 sds <- apply(quant_data_log, 1, 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
1547 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
1548 plot(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1549 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
1550 , 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
1551 , 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
1552 , 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
1553 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1554 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1555 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1556 "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
1557 "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
1558 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1559 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1560
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1561 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1562
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1563 ```{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
1564 # 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
1565 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
1566
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1567 # 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
1568 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
1569
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1570 # 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
1571 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
1572 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
1573 ```
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1574
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1575 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1576
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1577 # 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
1578
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1579 ```
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1580 # Impute 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
1581
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1582 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1583
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1584 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
1585 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
1586 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
1587
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1588 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1589
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1590 ```{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
1591 #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
1592
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1593 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1594 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1595
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1596 # 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
1597 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
1598
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1599 ```
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1600 ```{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
1601
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1602 # Apply imputation
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1603 switch(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1604 imputation_method
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1605 , "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
1606 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
1607 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
1608 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
1609 "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
1610 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1611 sample_level_integers <- as.integer(sample_treatment_levels)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1612 # 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
1613 # 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
1614 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
1615 for (i in seq_len(length(levels(sample_treatment_levels)))) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1616 # 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
1617 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
1618 # 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
1619 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
1620 # 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
1621 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
1622 # 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
1623 # 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
1624 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
1625 the_centers <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1626 apply(lvlsbst, 1, median, 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
1627 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
1628 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
1629 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
1630 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
1631 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1632 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1633 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1634 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
1635 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1636 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1637 # 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
1638 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
1639 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
1640 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1641 , "median" = {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1642 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
1643 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
1644 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
1645 "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
1646 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1647 # 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
1648 # 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
1649 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
1650 quant_data_imp[ind] <- apply(quant_data_imp, 1, median, na.rm = TRUE)[ind[, 1]]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1651 # 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
1652 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
1653 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
1654 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1655 , "mean" = {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1656 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
1657 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
1658 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
1659 "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
1660 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1661 # 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
1662 # 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
1663 # 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
1664 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
1665 # Assign to NA cells the mean for the row
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1666 quant_data_imp[ind] <- apply(quant_data_imp, 1, mean, na.rm = TRUE)[ind[, 1]]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1667 # 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
1668 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
1669 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
1670 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1671 , "random" = {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1672 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
1673 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
1674 # 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
1675 # 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
1676 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
1677 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
1678 sprintf(
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1679 "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
1680 q1, m1
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1681 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1682 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1683 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
1684 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
1685 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
1686 sd_percentile))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1687 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
1688 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
1689 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
1690 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
1691 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1692 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1693 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
1694
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1695 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
1696 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
1697 return(-1)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1698 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1699 ```
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1700
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1701 ```{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
1702 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
1703 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1704
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1705 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1706
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1707 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
1708 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
1709 imp_smry_missing_values_after <- sum(is.na(quant_data_imp[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
1710 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1711 ```{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
1712 # 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
1713 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
1714 "\\begin{table}[hb]", # h(inline); b(bottom); t (top) or p (separate page)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1715 " \\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
1716 " \\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
1717 " \\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
1718 " \\hline\\hline",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1719 " \\ & 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
1720 " 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
1721 " \\hline",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1722 " before imputation & %d & %d (%d\\%s) & \\\\",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1723 " after imputation & %d & %d & %d \\\\ [1ex]",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1724 " \\hline",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1725 " \\end{tabular}",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1726 #" \\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
1727 "\\end{table}",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1728 sep = "\n"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1729 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1730 tabular_lines <-
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1731 sprintf(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1732 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
1733 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
1734 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
1735 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
1736 "%",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1737 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
1738 imp_smry_missing_values_after,
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1739 imp_smry_rejected_after
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1740 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1741 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
1742 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1743 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1744
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1745
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1746 # Zap rows where imputation was ineffective
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1747 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
1748 quant_data <- quant_data [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
1749
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1750 quant_data_imp <- quant_data_imp[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
1751 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
1752 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
1753
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1754 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
1755 ```
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1756
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1757 ```{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
1758
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1759 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
1760 d_combined <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1761 as.numeric(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1762 as.matrix(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1763 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
1764 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1765 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1766 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
1767 as.numeric(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1768 as.matrix(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1769 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
1770 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1771 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1772
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1773 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
1774 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
1775 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1776 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
1777 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1778 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
1779 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
1780 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1781 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
1782 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1783
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1784 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
1785 # 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
1786 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
1787 as.numeric(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1788 as.matrix(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1789 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
1790 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1791 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1792 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
1793 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
1794 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1795 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
1796 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1797 } else {
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1798 # 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
1799 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
1800 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1801
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1802 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1803
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1804 ```{r echo = FALSE, fig.dim = c(9, 5.5), 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
1805 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
1806 rownames(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
1807 is.na((apply(quant_data_imp, 1, sd, na.rm = TRUE)) == 0)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1808 ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1809
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1810 if (length(zero_sd_rownames) >= nrow(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
1811 stop("All peptides have zero standard deviation. Cannot continue.")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1812 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1813 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
1814 cat(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1815 sprintf("%d peptides with zero variance were removed from statistical consideration",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1816 length(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
1817 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1818 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1819 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
1820 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
1821 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1822 quant_data_imp <- zap_named_rows(quant_data_imp, 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
1823 quant_data <- zap_named_rows(quant_data, 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
1824 full_data <- zap_named_rows(full_data, 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
1825 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1826
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1827 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
1828 cat("\\leavevmode\\newpage\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1829 # data visualization
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1830 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
1831 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
1832 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1833 # 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
1834 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
1835 # 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
1836 # - 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
1837 # - 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
1838 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
1839 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
1840 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
1841 # 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
1842 # 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
1843 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
1844
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1845 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
1846
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1847 # 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
1848 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
1849 # 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
1850 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
1851
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1852 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
1853 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
1854 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
1855 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
1856 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
1857 )
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1858 show_stripchart <-
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1859 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
1860 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
1861 boxplot_sub <- "Light blue = data before imputation; Red = imputed data"
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1862 } else {
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1863 boxplot_sub <- ""
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1864 }
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1865
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1866 # Vertical plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1867 colnames(blue_dots) <- 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
1868 boxplot(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1869 blue_dots
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1870 , las = 2 # "always vertical"
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1871 , cex.axis = 0.9 * sample_name_shrink
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1872 , col = const_boxplot_fill
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1873 , ylim = ylim
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1874 , main = "Peptide intensities after eliminating unusable peptides"
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1875 , sub = boxplot_sub
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1876 , 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
1877 , ylab = 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
1878 )
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1879
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1880 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
1881 # Points
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1882 # 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
1883 # 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
1884 stripchart(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1885 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
1886 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
1887 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
1888 pch = 19, # Pch symbols
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1889 cex = const_stripsmall_cex, # Size of symbols reduced
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1890 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
1891 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
1892 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
1893 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1894 stripchart(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1895 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
1896 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
1897 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
1898 pch = 19, # Pch symbols
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1899 cex = const_stripsmall_cex, # Size of symbols reduced
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1900 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
1901 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
1902 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
1903 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1904
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1905 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1906 if (TRUE) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1907 # show measured values in blue on left half-violin plot
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1908 cat("\\leavevmode\n\\quad\n\n\\quad\n\n")
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1909 vioplot::vioplot(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1910 x = lapply(blue_dots, function(x) x[!is.na(x)]),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1911 col = "lightblue1",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1912 side = "left",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1913 plotCentre = "line",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1914 ylim = ylim_save,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1915 main = "Distributions of observed and imputed data",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1916 sub = "Light blue = observed data; Pink = imputed data",
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1917 las = 2,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
1918 cex.axis = 0.9 * sample_name_shrink,
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1919 xlab = "Sample",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1920 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
1921 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1922 red_violins <- lapply(red_dots, function(x) x[!is.na(x)])
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1923 cols_to_delete <- c()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1924 for (ix in seq_len(length(red_violins))) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1925 if (length(red_violins[[ix]]) < 1) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1926 cols_to_delete <- c(cols_to_delete, ix)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1927 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1928 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1929 # destroy any unimputable columns
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1930 if (!is.null(cols_to_delete)) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1931 red_violins <- red_violins[-cols_to_delete]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1932 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1933 # plot imputed values in red on right half-violin plot
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1934 vioplot::vioplot(
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1935 x = red_violins,
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1936 col = "lightpink1",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1937 side = "right",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1938 plotCentre = "line",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1939 add = TRUE
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1940 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1941 }
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1942
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1943 par(old_par)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1944
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1945 # density plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1946 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
1947 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
1948 ylim <- c(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1949 0,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1950 max(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1951 if (is.list(d_combined)) d_combined$y else d_combined,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1952 if (is.list(d_original)) d_original$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
1953 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
1954 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
1955 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
1956 )
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1957 plot(
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
1958 d_combined,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
1959 ylim = ylim,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
1960 sub =
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1961 paste(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
1962 "Blue = data before imputation; Red = imputed data;",
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
1963 "Black = combined"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
1964 ),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
1965 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"
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parents: 14
diff changeset
1966 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"
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parents: 12
diff changeset
1967 ylab = "Probability density"
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
1968 )
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
1969 lines(d_original, col = "blue")
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
1970 lines(d_imputed, col = "red")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
1971 } else {
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
1972 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1973 "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"
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parents: 12
diff changeset
1974 "before and after imputation."
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
1975 )
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
1976 }
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
1977 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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parents: 12
diff changeset
1978 }
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
1979 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
1980
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
1981 # Perform Quantile Normalization
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
1982
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
1983 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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parents: 15
diff changeset
1984 *[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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parents: 15
diff changeset
1985 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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parents: 15
diff changeset
1986 DOI *[10.1093/bioinformatics/19.2.185](https://doi.org/10.1093%2Fbioinformatics%2F19.2.185)*
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
1987 and *its supplementary material [http://bmbolstad.com/misc/normalize/normalize.html](http://bmbolstad.com/misc/normalize/normalize.html)*,
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
1988 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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parents: 15
diff changeset
1989 subtle differences among grossly similar samples (having similar distributions)
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
1990 by equailzing intra-quantile quantitations.
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
1991 Unfortunately, one software library upon which it depends
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
1992 *[suffers from a concurrency defect](https://support.bioconductor.org/p/122925/#9135989)*
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
1993 that requires that a specific, non-concurrent version of the library be
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
1994 installed. The installation command equivalent to what was used to install the library to produce the results presented here is:
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
1995 ```
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
1996 conda install bioconductor-preprocesscore openblas=0.3.3
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
1997 ```
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
1998
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1999
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
2000 <!--
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
2001 # Apply quantile normalization using preprocessCore::normalize.quantiles
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2002 # ---
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2003 # tool repository: http://bioconductor.org/packages/release/bioc/html/preprocessCore.html
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2004 # except this: https://support.bioconductor.org/p/122925/#9135989
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2005 # says to install it like this:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2006 # ```
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
2007 # BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE, lib=.libPaths()[1])
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
2008 # ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2009 # conda installation (necessary because of a bug in recent openblas):
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2010 # conda install bioconductor-preprocesscore openblas=0.3.3
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2011 # ...
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
2012 # ---
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
2013 # normalize.quantiles {preprocessCore} -- Quantile Normalization
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
2014 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2015 # Description:
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
2016 # Using a normalization based upon quantiles, this function normalizes a
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
2017 # matrix of probe level intensities.
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
2018 #
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
2019 # THIS FUNCTIONS WILL HANDLE MISSING DATA (ie NA values), based on the
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
2020 # assumption that the data is missing at random.
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
2021 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2022 # Usage:
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
2023 # normalize.quantiles(x, copy = TRUE, keep.names = FALSE)
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
2024 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2025 # Arguments:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2026 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2027 # - x: A matrix of intensities where each column corresponds to a chip and each row is a probe.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2028 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2029 # - copy: Make a copy of matrix before normalizing. Usually safer to work with a copy,
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2030 # but in certain situations not making a copy of the matrix, but instead normalizing
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2031 # it in place will be more memory friendly.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2032 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2033 # - keep.names: Boolean option to preserve matrix row and column names in output.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2034 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2035 # Details:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2036 # This method is based upon the concept of a quantile-quantile plot extended to n dimensions.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2037 # No special allowances are made for outliers. If you make use of quantile normalization
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2038 # please cite Bolstad et al, Bioinformatics (2003).
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2039 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2040 # This functions will handle missing data (ie NA values), based on
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
2041 # the assumption that the data is missing at random.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2042 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2043 # Note that the current implementation optimizes for better memory usage
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2044 # at the cost of some additional run-time.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2045 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2046 # Value: A normalized matrix.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2047 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2048 # Author: Ben Bolstad, bmbolstad.com
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2049 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2050 # References
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2051 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2052 # - Bolstad, B (2001) Probe Level Quantile Normalization of High Density Oligonucleotide
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2053 # Array Data. Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2054 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2055 # - Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) A Comparison of
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2056 # Normalization Methods for High Density Oligonucleotide Array Data Based on Bias
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2057 # and Variance. Bioinformatics 19(2), pp 185-193. DOI 10.1093/bioinformatics/19.2.185
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2058 # http://bmbolstad.com/misc/normalize/normalize.html
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2059 # ...
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2060 -->
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2061 ```{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
2062
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2063 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
2064 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
2065 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
2066 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2067 } else {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2068 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
2069 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2070
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2071 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
2072
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2073 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
2074
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2075 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
2076
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2077 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
2078
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2079 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
2080
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2081 sel <- apply(quant_data_imp_qn_ls, 1, 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
2082 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
2083
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2084 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
2085 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
2086
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2087 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
2088
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2089 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
2090 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
2091
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2092 # 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
2093 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
2094 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2095
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2096 <!-- ACE insertion begin -->
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2097 ## 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
2098
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2099 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'}
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2100
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2101 # 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
2102 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
2103
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2104 # 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
2105 # 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
2106 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
2107 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
2108
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2109 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
2110
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2111 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
2112 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2113 sprintf(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2114 "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
2115 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
2116 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2117 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2118 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
2119
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2120
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2121 # data visualization
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2122 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
2123 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
2124 , 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
2125 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2126 # 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
2127 # Vertical plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2128 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
2129 boxplot(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2130 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
2131 , las = 2
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2132 , cex.axis = 0.9 * sample_name_shrink
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2133 , 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
2134 , 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
2135 , xlab = "Sample"
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2136 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2137 par(old_par)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2138 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2139 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
2140 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2141
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2142 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
2143
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2144 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2145
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2146 ```{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
2147 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
2148 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
2149 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
2150 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
2151 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
2152 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
2153 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2154 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
2155 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2156 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2157 ```{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
2158 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
2159 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2160
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2161 # ANOVA Analysis
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2162
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2163 ```{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
2164 # 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
2165 # 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
2166 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
2167 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
2168 , 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
2169 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2170 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
2171 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2172
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2173 ```{r anova, echo = FALSE, fig.dim = c(9, 10), 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
2174 count_of_treatment_levels <- length(levels(sample_treatment_levels))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2175 if (count_of_treatment_levels < 2) {
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2176 nuke_control_sequences <-
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2177 function(s) {
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2178 s <- gsub("[\\]", "xyzzy_plugh", s)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2179 s <- gsub("[$]", "\\\\$", s)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2180 s <- gsub("xyzzy_plugh", "$\\\\backslash$", s)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2181 return(s)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2182 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2183 cat(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2184 "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
2185 "(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
2186 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2187 cat(
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2188 "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
2189 "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
2190 )
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2191
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2192 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
2193 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
2194 "\\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
2195 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
2196 "\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
2197
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2198 regex_sample_names <- nuke_control_sequences(regex_sample_names)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2199
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2200 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
2201 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
2202 "\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
2203 "\\text{'",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2204 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
2205 "'}\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
2206 sep = ""
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2207 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2208
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2209 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
2210 "\\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
2211 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
2212 "\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
2213
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2214 regex_sample_grouping <- nuke_control_sequences(regex_sample_grouping)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2215
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2216 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
2217 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
2218 "\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
2219 "\\text{'",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2220 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
2221 "'}\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
2222 sep = ""
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2223 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2224
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2225 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
2226 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
2227 "\\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
2228 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
2229 "\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
2230
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2231 } else {
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2232
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2233 p_value_data_anova_ps <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2234 apply(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2235 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
2236 1,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2237 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
2238 grouping_factor = sample_treatment_levels,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2239 one_way_f = one_way_all_categories
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2240 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2241
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2242 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
2243 p.adjust(p_value_data_anova_ps, method = "fdr")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2244 p_value_data <- data.frame(
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2245 phosphopeptide = full_data[, 1],
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2246 raw_anova_p = p_value_data_anova_ps,
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2247 fdr_adjusted_anova_p = p_value_data_anova_ps_fdr
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2248 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2249
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2250 # 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
2251 # e.g. "Outputfile_pST_ANOVA_STEP5.txt"
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2252 # becomes "Outpufile_pST_ANOVA_STEP5_FDR0.05.txt"
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2253
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2254 # Re-output datasets to include p-values
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2255 metadata_plus_p <- cbind(full_data[1:9], p_value_data[, 2:3])
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2256 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
2257 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
2258 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
2259 sep = "\t",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2260 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
2261 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
2262 quote = FALSE
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2263 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2264
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2265 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
2266 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
2267 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
2268 sep = "\t",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2269 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
2270 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
2271 quote = FALSE
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2272 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2273
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2274
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2275 p_value_data <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2276 p_value_data[order(p_value_data$fdr_adjusted_anova_p), ]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2277
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2278 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
2279 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
2280 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
2281 for (cutoff in val_fdr) {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2282 if (number_of_peptides_found > 49) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2283 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
2284 break
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2285 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2286
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2287 #loop through FDR cutoffs
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2288
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2289 filtered_p <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2290 p_value_data[
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2291 which(p_value_data$fdr_adjusted_anova_p < cutoff),
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2292 , 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
2293 ]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2294 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
2295 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
2296 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
2297 , 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
2298 ]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2299 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
2300 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
2301 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
2302 , 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
2303 ]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2304
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2305 # <!-- ACE insertion start -->
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2306
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2307 if (nrow(filtered_p) && nrow(filtered_data_filtered) > 0) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2308 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
2309 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
2310 } else {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2311 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
2312 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2313 if (nrow(filtered_data_filtered) > 1) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2314 subsection_header(sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2315 "Intensity distributions for %d phosphopeptides whose adjusted p-value < %0.2f\n",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2316 nrow(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
2317 cutoff
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2318 ))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2319 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2320 subsection_header(sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2321 "Intensity distribution for one phosphopeptide (%s) whose adjusted p-value < %0.2f\n",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2322 rownames(filtered_data_filtered)[1],
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2323 cutoff
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2324 ))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2325 }
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2326 cat("\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
2327 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
2328
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2329 old_oma <- par("oma")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2330 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
2331 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
2332 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
2333 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
2334 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
2335 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
2336 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2337 # 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
2338 # Vertical plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2339 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
2340 tryCatch(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2341 boxplot(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2342 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
2343 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
2344 las = 2,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2345 cex.axis = 0.9 * sample_name_shrink,
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2346 col = const_boxplot_fill,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2347 ylab = 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
2348 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2349 error = function(e) print(e)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2350 )
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2351 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
2352 } else {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2353 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
2354 "%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
2355 "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
2356 cutoff
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2357 ))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2358 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2359
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2360 if (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
2361 # 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
2362 # 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
2363 # 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
2364 # 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
2365 # error upstream.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2366 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
2367 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
2368 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
2369 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
2370 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
2371 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2372 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
2373
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2374 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
2375 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
2376 intense = anova_filtered_merge$Intensity,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2377 data = anova_filtered_merge[, 2:number_of_samples + 1]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2378 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2379 colnames(anova_filtered) <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2380 c("Phosphopeptide", colnames(filtered_data_filtered))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2381
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2382 # Merge qualitative columns into the ANOVA data
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2383 output_table <- data.frame(anova_filtered$Phosphopeptide)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2384 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
2385 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
2386 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
2387 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
2388 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
2389 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2390
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2391 # 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
2392
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2393 anova_filtered_merge_format <- sapply(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2394 X = filtered_p$fdr_adjusted_anova_p
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2395 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2396 FUN = function(x) {
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2397 if (x > 0.01)
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2398 paste0("%s (%0.", 1 + ceiling(-log10(x)), "f)")
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2399 else
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2400 paste0("%s (%0.2e)")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2401 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2402 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2403
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2404 cat_hm_heading <- function(m, cutoff) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2405 if (nrow(m) > 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
2406 cat("\\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
2407 subsection_header(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2408 paste(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2409 sprintf("Heatmap for the %d most-significant peptides",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2410 intensity_hm_rows),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2411 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
2412 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2413 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2414 } else {
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2415 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
2416 return(FALSE)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2417 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2418 subsection_header(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2419 paste(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2420 sprintf("Heatmap for %d usable peptides whose", nrow(m)),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2421 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
2422 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2423 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2424 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2425 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2426 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
2427 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
2428 return(TRUE)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2429 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2430
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2431 # 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
2432 m <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2433 as.matrix(unimputed_quant_data_log[anova_filtered_merge_order, ])
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2434 if (nrow(m) > 0) {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2435 rownames_m <- rownames(m)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2436 rownames(m) <- sapply(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2437 X = seq_len(nrow(m))
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2438 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2439 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
2440 sprintf(
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
2441 anova_filtered_merge_format[i],
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2442 rownames_m[i],
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2443 signif(filtered_p$fdr_adjusted_anova_p[i], 2)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2444 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2445 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2446 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2447 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2448 # draw the heading and heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2449 if (nrow(m) > 0) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2450 number_of_peptides_found <-
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2451 draw_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
2452 m = m,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2453 cutoff = cutoff,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2454 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
2455 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
2456 "log(intensities), row-scaled, unimputed, unnormalized",
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2457 suppress_row_dendrogram = FALSE
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
2458 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
2459 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2460 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2461 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
2462 }
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2463 cat("\\leavevmode\n")
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
2464 cat("The adjusted ANOVA \\textit{p}-value is shown in parentheses
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
2465 after the phosphopeptide sequence.\n\n")
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
2466 ```
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2467
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
2468 ```{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
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parents: 15
diff changeset
2469
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2470 if (count_of_treatment_levels > 1) {
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
2471 # 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
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parents: 15
diff changeset
2472 # Strategy:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2473 # - 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
2474 # - 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
2475 # - 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
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parents: 15
diff changeset
2476 # - 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
2477 # - 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
2478 # - 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
2479 # 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
2480 # - 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
2481 # - 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
2482 # (# 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
2483
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2484 # 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
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parents: 15
diff changeset
2485 m2 <- combn(
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
2486 x = seq_len(length(levels(sample_treatment_levels))),
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
2487 m = 2,
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
2488 simplify = TRUE
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
2489 )
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
2490 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
2491
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
2492 # 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
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parents: 15
diff changeset
2493 # - 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
2494 # - 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
2495 f_m2 <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2496 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
2497 return(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2498 data.frame(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2499 contrast = cntrst,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2500 level = sample_treatment_levels[
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2501 sample_treatment_levels %in%
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2502 levels(sample_treatment_levels)[c(lvl1, lvl2)]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2503 ],
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2504 label = sample_name_matches[
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2505 sample_treatment_levels %in%
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2506 levels(sample_treatment_levels)[c(lvl1, lvl2)]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2507 ]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2508 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2509 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2510 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2511 # - 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
2512 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
2513 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
2514 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
2515 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2516 # - 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
2517 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
2518
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2519 # - 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
2520 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
2521
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2522 # - 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
2523 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
2524
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2525 RSQLite::dbWriteTable(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2526 conn = db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2527 name = "contrast",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2528 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
2529 overwrite = TRUE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2530 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2531
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2532 # 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
2533 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
2534 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
2535 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
2536 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2537 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2538 # 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
2539 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
2540 -- 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
2541 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
2542 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
2543 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2544 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2545 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
2546 -- 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
2547 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
2548 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
2549 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2550 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2551 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
2552 -- 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
2553 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
2554 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
2555 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2556 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2557 # - 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
2558 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
2559
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2560 # 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
2561 # - 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
2562 # - 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
2563 casted <- cbind(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2564 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
2565 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
2566 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2567 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
2568 casted,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2569 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
2570 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2571 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
2572 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
2573 # - 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
2574 rm(casted)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2575
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2576 # - 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
2577 RSQLite::dbWriteTable(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2578 conn = db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2579 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
2580 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
2581 overwrite = TRUE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2582 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2583 # 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
2584 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
2585 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
2586 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
2587 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2588 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2589 # 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
2590 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
2591 -- 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
2592 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
2593 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
2594 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2595 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2596 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
2597 -- 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
2598 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
2599 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
2600 "
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 # - 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
2603 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
2604
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2605 # - 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
2606 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
2607 -- 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
2608 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
2609 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2610 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2611 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
2612 -- 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
2613 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
2614 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2615 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2616 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
2617 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
2618 "
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 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
2621 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
2622 "
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 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
2625 -- 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
2626 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
2627 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2628 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2629 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
2630 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
2631 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2632 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2633 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
2634 -- 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
2635 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
2636 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2637 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2638 # - create view
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2639 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
2640 -- 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
2641 -- 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
2642 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
2643 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2644 SELECT contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2645 level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2646 phosphopep,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2647 sample,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2648 quant
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2649 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
2650 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
2651 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
2652 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
2653 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2654 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2655 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2656 # - 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
2657 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
2658 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
2659 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2660 SELECT contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2661 level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2662 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
2663 FROM contrast
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2664 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
2665 /* 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
2666 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
2667 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2668 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2669 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2670 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
2671 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
2672 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2673 SELECT contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2674 level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2675 phosphopep,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2676 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
2677 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
2678 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
2679 /* 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
2680 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
2681 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2682 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2683 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2684
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2685 # - create contrast-metadata table
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2686 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
2687 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
2688 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2689 SELECT DISTINCT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2690 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
2691 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
2692 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
2693 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
2694 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
2695 '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
2696 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
2697 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
2698 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
2699 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
2700 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
2701 /* 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
2702 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
2703 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2704 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2705 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2706 # - 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
2707 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
2708 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
2709 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2710 SELECT DISTINCT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2711 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
2712 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
2713 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
2714 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
2715 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
2716 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
2717 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
2718 /* 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
2719 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
2720 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2721 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2722 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2723
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2724 # - 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
2725 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
2726 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
2727 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2728 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
2729 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
2730 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
2731 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
2732 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
2733 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
2734 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
2735 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
2736 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
2737 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
2738 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
2739 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
2740 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
2741 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
2742 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
2743 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
2744 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
2745 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
2746 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
2747 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
2748 /* 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
2749 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2750 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2751 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2752
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2753 # 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
2754 # 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
2755 # - 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
2756 # 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
2757 # - 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
2758 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
2759 invisible(contrast)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2760 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2761 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
2762 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
2763 x = paste0("
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2764 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
2765 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
2766 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
2767 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
2768 "),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2769 connection = db
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2770 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2771 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
2772 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
2773 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
2774 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
2775 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2776 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
2777 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
2778 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
2779
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2780 # - 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
2781 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
2782 x = paste0("
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2783 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
2784 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
2785 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
2786 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
2787 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
2788 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2789 connection = db
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2790 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2791 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
2792 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
2793
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2794 # - 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
2795 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
2796 apply(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2797 X = 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
2798 MARGIN = 1, # apply to rows
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2799 FUN = anova_func,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2800 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
2801 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
2802 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
2803 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
2804 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2805 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
2806 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
2807 method = "fdr",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2808 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
2809 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2810 # - 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
2811 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
2812 data.frame(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2813 contrast = contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2814 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
2815 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
2816 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
2817 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2818 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
2819 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
2820 RSQLite::dbWriteTable(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2821 conn = db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2822 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
2823 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
2824 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
2825 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2826 # 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
2827 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
2828 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
2829 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
2830 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2831 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2832 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2833 # 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
2834 # 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
2835 # 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
2836 # 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
2837 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
2838 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
2839 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2840 SELECT *
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2841 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
2842 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
2843 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2844 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2845 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2846 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
2847 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
2848 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2849 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
2850 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
2851 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
2852 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
2853 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
2854 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
2855 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2856 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2857 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2858 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
2859 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
2860 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2861 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2862 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2863 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
2864 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
2865 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2866 SELECT a.*,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2867 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
2868 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
2869 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
2870 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
2871 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
2872 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
2873 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
2874 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2875 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2876 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2877 # Create UK
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2878 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
2879 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
2880 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
2881 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2882 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2883 # 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
2884 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
2885 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
2886 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
2887 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2888 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2889 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
2890 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
2891 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
2892 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2893 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2894 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
2895 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
2896 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
2897 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2898 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2899 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
2900 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
2901 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
2902 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2903 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2904 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
2905 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
2906 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2907 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2908 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2909 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
2910 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
2911 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2912 SELECT contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2913 a_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2914 a_samples,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2915 b_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2916 b_samples,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2917 a_quant,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2918 b_quant,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2919 fc_description,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2920 log2_fc,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2921 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
2922 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
2923 phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2924 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
2925 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
2926 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2927 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2928 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2929 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
2930 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
2931 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2932 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2933 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2934 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
2935 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
2936 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2937 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
2938 SELECT DISTINCT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2939 deppep.seq,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2940 ppep.seq,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2941 GeneName||';',
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2942 UniProtID||';',
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2943 PhosphoResidue||';'
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2944 FROM
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2945 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
2946 WHERE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2947 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
2948 AND
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2949 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
2950 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2951 SELECT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2952 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
2953 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
2954 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
2955 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
2956 REPLACE(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2957 REPLACE(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2958 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
2959 'p',
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2960 ''
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2961 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2962 ', ',
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2963 ';'
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2964 ) 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
2965 FROM extended
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2966 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2967 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2968 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2969 # 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
2970 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
2971 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
2972 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
2973 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2974 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2975 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
2976 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
2977 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2978 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2979 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2980 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
2981 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
2982 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2983 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
2984 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
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parents: 15
diff changeset
2985 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
2986 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2987 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2988 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2989 ddl_exec(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
2990 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
2991 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2992 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2993 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
2994 dml_no_rows_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2995 CREATE VIEW v_kseaapp_input
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
2996 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2997 SELECT v.contrast,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
2998 v.phosphopep,
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
2999 m.`Protein`,
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
3000 m.`Gene`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3001 m.`Peptide`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3002 m.`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
3003 v.p_value_raw AS `p`,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3004 v.log2_fc AS `FC`
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3005 FROM kseaapp_metadata AS m,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3006 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
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diff changeset
3007 WHERE m.ppep = v.phosphopep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3008 AND NOT m.`Gene` = 'No_Gene_Name'
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3009 AND NOT v.log2_fc = 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
3010 ;
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
3011 "
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
3012 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3013 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3014 ```
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
3015
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3016 ```{r echo = FALSE, results = 'asis'}
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3017 cat("\\newpage\n")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3018 ```
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3019
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3020 # KSEA Analysis
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3021
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3022 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
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diff changeset
3023
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3024 - 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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diff changeset
3025 - 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
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diff changeset
3026 - 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
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parents: 15
diff changeset
3027
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3028 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
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diff changeset
3029
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3030 $$
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3031 \text{kinase enrichment score}_{j,i} = \frac{(\overline{s}_{j,i} - \overline{p}_j)\sqrt{m_{j,i}}}{\delta_j}
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3032 $$
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3033
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3034 and fold-enrichment is computed as:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3035
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3036 $$
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3037 \text{Enrichment}_{j,i} = \frac{\overline{s}_{j,i}}{\overline{p}_j}
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3038 $$
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3039
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3040 where:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3041
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3042 - $\overline{s}_{j,i}$ is the mean $\log_2 (|\text{fold-change|})$ in intensities (for contrast $j$) of known substrates of the kinase $i$,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3043 - $\overline{p}_j$ is the mean $\log_2 (|\text{fold-change}|)$ of all phosphosites identified in contrast $j$, and
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3044 - $m_{j,i}$ is the total number of phosphosite substrates of kinase $i$ identified in contrast $j$,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3045 - $\delta_j$ is the standard deviation of the $\log_2 (|\text{fold-change}|)$ for contrast $j$ across all phosphosites in the dataset.
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3046 - 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
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diff changeset
3047
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3048 $\text{FDR}_{j,i}$ is computed from the $p$-value for the z-score using the R `stats::p.adjust` function, applying the False Discovery Rate 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)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3049
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3050 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
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diff changeset
3051
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3052 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
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diff changeset
3053
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3054 - 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
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diff changeset
3055 - 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)).
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3056 - Kinase-strate deata 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).
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3057
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3058 ```{r ksea, 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
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parents: 15
diff changeset
3059
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3060 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
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diff changeset
3061
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3062 # -- 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
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diff changeset
3063 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3064 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
3065 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3066
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3067 # -- 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
3068 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
3069 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
3070 id INTEGER PRIMARY KEY
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3071 , 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
3072 , 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
3073 , abbrev TEXT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3074 , pattern TEXT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3075 , motif TEXT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3076 );
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3077 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3078
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3079 # -- 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
3080 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
3081 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
3082 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
3083 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
3084 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
3085 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3086
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3087 # -- 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
3088 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
3089 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
3090 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3091
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3092 # -- 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
3093 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
3094 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
3095 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3096 SELECT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3097 '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
3098 '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
3099 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
3100 '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
3101 '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
3102 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
3103 '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
3104 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
3105 '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
3106 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
3107 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
3108 '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
3109 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
3110 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
3111 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
3112 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3113
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3114 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
3115 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
3116 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
3117 rslt$score_list <- list()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3118 rslt$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
3119 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
3120
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3121 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
3122 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
3123 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3124 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3125
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3126 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
3127 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
3128 "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
3129
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3130 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
3131 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
3132 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
3133 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
3134 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
3135 contrast_longlabel <- (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3136 sprintf(
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3137 "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
3138 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
3139 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
3140 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3141 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3142 kseaapp_input <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3143 sqldf::sqldf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3144 x = sprintf("
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3145 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
3146 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
3147 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
3148 ",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3149 i_cntrst
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3150 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3151 connection = db
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3152 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3153
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3154 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
3155
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3156 # 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
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parents: 15
diff changeset
3157 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
3158 main_title <- (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3159 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3160 "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
3161 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
3162 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
3163 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3164 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3165 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
3166 tryCatch(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3167 expr = {
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
3168 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
3169 ksea_scores(
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
3170 ksdata = pseudo_ksdata, # KSEAapp::KSData,
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
3171 px = kseaapp_input,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3172 networkin = TRUE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3173 networkin_cutoff = 2
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3174 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3175
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3176 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
3177 next_index <- 1 + next_index
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
3178 rslt$score_list[[next_index]] <- ksea_scores_rslt
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
3179 rslt$name_list[[next_index]] <- contrast_label
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
3180 rslt$longname_list[[next_index]] <- contrast_longlabel
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
3181 low_fdr_print(
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
3182 rslt = 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
3183 i_cntrst = 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
3184 i = next_index,
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
3185 a_level = cntrst_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
3186 b_level = cntrst_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
3187 fold_change = cntrst_fold_change,
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
3188 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
3189 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3190 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3191 },
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3192 error = function(e) str(e)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3193 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3194 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3195
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3196 plotted_kinases <- NULL
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
3197 if (length(rslt$score_list) > 1) {
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
3198 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
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diff changeset
3199 hdr <- ksea_heatmap_titles[[i]]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3200 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
3201
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3202 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
3203 if (i == 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
3204 subsection_header(hdr)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3205 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3206 subsection_header(hdr)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3207 }
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
3208 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
3209
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3210 plotted_kinases <- ksea_heatmap(
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
3211 # 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
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diff changeset
3212 score_list = rslt$score_list,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
3213 # a character vector of all the sample names for heatmap annotation:
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
3214 # - the names must be in the same order as the data in score_list
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
3215 # - please avoid long names, as they may get cropped in the final image
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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parents: 15
diff changeset
3216 sample_labels = rslt$name_list,
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
3217 # 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
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diff changeset
3218 # to use for marking statistically significant scores
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3219 stats = c("p.value", "FDR")[2],
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
3220 # 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
3221 # 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
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diff changeset
3222 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
3223 # 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
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parents: 15
diff changeset
3224 # for indicating significant kinases in 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
3225 p_cutoff = 0.05,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3226 # 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
3227 # hierarchical clustering of the sample columns
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3228 sample_cluster = TRUE,
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
3229 # 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
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parents: 15
diff changeset
3230 # 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
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diff changeset
3231 export = FALSE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3232 # 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
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diff changeset
3233 # - main: main title of plot
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3234 # - 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
3235 # - 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
3236 xlab = "Contrast",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3237 ylab = "Kinase",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3238 # 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
3239 # - 1 : all 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
3240 # - 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
3241 # - 3 : non-significant kinases
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3242 which_kinases = 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
3243 )
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3244 if (!is.null(plotted_kinases)) {
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
3245 cat("\\begin{center}\n")
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
3246 cat("Color intensity reflects $z$-score magnitudes; hue reflects $z$-score sign. Asterisks reflect significance.\n")
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
3247 cat("\\end{center}\n")
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
3248 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3249 } # end for (i in ...
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
3250 } # end if (length ...
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3251
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
3252 for (i_cntrst in seq_len(length(rslt$score_list))) {
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
3253 next_index <- 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
3254 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
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diff changeset
3255 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
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parents: 15
diff changeset
3256 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
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parents: 15
diff changeset
3257 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
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diff changeset
3258 contrast_longlabel <- (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3259 sprintf(
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3260 "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
3261 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
3262 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
3263 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3264 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3265 main_title <- (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3266 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3267 "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
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diff changeset
3268 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
3269 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
3270 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3271 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
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diff changeset
3272 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
3273 tryCatch(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3274 expr = {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3275 ksea_scores_rslt <- rslt$score_list[[next_index]]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3276
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3277 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
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diff changeset
3278 low_fdr_barplot(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3279 rslt = rslt,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3280 i_cntrst = 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
3281 i = next_index,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3282 a_level = cntrst_a_level,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3283 b_level = cntrst_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
3284 fold_change = cntrst_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
3285 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
3286 )
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
3287 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3288 },
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3289 error = function(e) str(e)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3290 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3291 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3292 ```
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3293
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3294 ```{r enriched, 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
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parents: 15
diff changeset
3295
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3296 # Use enriched kinases to find enriched kinase-substrate pairs
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
3297 enriched_kinases <- data.frame(kinase = ls(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
3298 all_enriched_substrates <- sqldf("
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3299 SELECT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3300 gene AS kinase,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3301 ppep,
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3302 sub_gene,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
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diff changeset
3303 '('||group_concat(gene||'-'||sub_gene)||') '||ppep AS label,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3304 fdr_adjusted_anova_p
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3305 FROM (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
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diff changeset
3306 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
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diff changeset
3307 FROM pseudo_ksdata
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
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diff changeset
3308 WHERE gene IN (SELECT kinase FROM enriched_kinases)
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3309 ),
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3310 p_value_data
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
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diff changeset
3311 WHERE ppep = phosphopeptide
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3312 GROUP BY 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
3313 ORDER BY fdr_adjusted_anova_p
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3314 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3315
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3316 # helper used to label per-kinase substrate enrichment figure
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3317 cat_enriched_heading <- function(m, 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
3318 cutoff <- cut_args$cutoff
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3319 kinase <- cut_args$kinase
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3320 statistic <- cut_args$statistic
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3321 threshold <- cut_args$threshold
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3322 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
3323 if (nrow(m) > intensity_hm_rows) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3324 subsection_header(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3325 paste(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3326 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3327 "Lowest p-valued %d (of %d) enriched %s-substrates,",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3328 intensity_hm_rows,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3329 nrow(m),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3330 kinase
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3331 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3332 sprintf(" KSEA %s < %0.2f\n", statistic, threshold)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3333 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3334 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3335 } else {
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3336 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
3337 return(FALSE)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3338 } else {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3339 subsection_header(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3340 paste(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3341 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3342 "%d enriched %s-substrates,",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3343 nrow(m),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3344 kinase
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3345 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3346 sprintf(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3347 " KSEA %s < %0.2f\n",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3348 statistic,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3349 threshold
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3350 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3351 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3352 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3353 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3354 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3355 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
3356 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
3357 return(TRUE)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3358 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3359
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3360 # Disabling heatmaps for substrates pending decision whether to eliminate them altogether
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3361 if (TRUE)
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3362 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
eschen42
parents: 15
diff changeset
3363 enriched_substrates <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3364 all_enriched_substrates[
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3365 all_enriched_substrates$kinase == kinase_name,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3366 ,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3367 drop = FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3368 ]
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3369 enriched_substrates$label <- with(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3370 enriched_substrates,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3371 sprintf(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3372 "(%s-%s) %s (%0.2g)",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3373 kinase,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3374 sub("$FAILED_MATCH_GENE_NAME", "unidentified", sub_gene, fixed = TRUE),
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3375 ppep,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3376 fdr_adjusted_anova_p
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3377 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3378 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3379 # Get the intensity values for the heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3380 enriched_intensities <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3381 as.matrix(unimputed_quant_data_log[enriched_substrates$ppep, , drop = FALSE])
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3382 # Remove rows having too many NA values to be relevant
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3383 # Rename the rows with the display-name for the heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3384 rownames(enriched_intensities) <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3385 sapply(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3386 X = rownames(enriched_intensities),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3387 FUN = function(rn) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3388 enriched_substrates[enriched_substrates$ppep == rn, "label"]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3389 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3390 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3391 # Format as matrix for heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3392 m <- as.matrix(enriched_intensities)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3393 # Draw the heading and heatmap
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3394 if (nrow(m) > 0) {
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3395 cut_args <- new_env()
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3396 cut_args$cutoff <- cutoff
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3397 cut_args$kinase <- kinase_name
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3398 cut_args$statistic <- 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
3399 cut_args$threshold <- 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
3400 number_of_peptides_found <-
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3401 draw_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
3402 m = m,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3403 cutoff = cut_args,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3404 hm_heading_function = cat_enriched_heading,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3405 hm_main_title
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3406 = "Unnormalized (zero-imputed) intensities of enriched kinase-substrates",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3407 suppress_row_dendrogram = FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3408 )
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3409 if (number_of_peptides_found > 1) {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3410 cat("\\leavevmode\n")
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3411 cat("The kinase-subsrate pair is shown in parentheses
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3412 before the phosphopeptide sequence.\n\n")
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3413 cat("The adjusted ANOVA \\textit{p}-value is shown in parentheses
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3414 after the phosphopeptide sequence.\n\n")
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3415 }
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3416 if (nrow(m) == 1) {
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3417 cat(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3418 sprintf(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3419 "\n\nSubstrate is %s,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3420 \nphopshopeptide is %s,
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3421 \n\nand adjusted ANOVA \\textit{p}-value is %0.2g.\n",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3422 enriched_substrates[1, "sub_gene"],
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3423 enriched_substrates[1, "ppep"],
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3424 enriched_substrates[1, "fdr_adjusted_anova_p"]
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3425 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3426 )
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3427 }
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3428 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3429 }
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3430
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3431 # Write output tabular files
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3432
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3433 # get kinase, ppep, concat(kinase) tuples for enriched kinases
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3434
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3435 kinase_ppep_label <- sqldf("
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3436 WITH
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3437 t(ppep, label) AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3438 (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3439 SELECT DISTINCT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3440 SUB_MOD_RSD AS ppep,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3441 group_concat(gene, '; ') AS label
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3442 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
3443 WHERE GENE IN (SELECT kinase FROM enriched_kinases)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3444 GROUP BY ppep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3445 ),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3446 k(kinase, ppep_join) AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3447 (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3448 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep_join
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3449 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
3450 WHERE GENE IN (SELECT kinase FROM enriched_kinases)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3451 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3452 SELECT k.kinase, t.ppep, t.label
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3453 FROM t, k
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3454 WHERE t.ppep = k.ppep_join
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3455 ORDER BY k.kinase, t.ppep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3456 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3457
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3458 # extract what we need from full_data
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3459 impish <- cbind(rownames(quant_data_imp), 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
3460 colnames(impish)[1] <- "Phosphopeptide"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3461 data_table_imputed_sql <- "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3462 SELECT
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3463 f.*,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3464 k.label 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
3465 q.*
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3466 FROM
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3467 metadata_plus_p f
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3468 LEFT JOIN kinase_ppep_label k
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3469 ON f.Phosphopeptide = k.ppep,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3470 impish q
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3471 WHERE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3472 f.Phosphopeptide = q.Phosphopeptide
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3473 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3474 data_table_imputed <- sqldf(data_table_imputed_sql)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3475 # Zap the duplicated 'Phosphopeptide' column named 'ppep'
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3476 data_table_imputed <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3477 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3478
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3479 # Output with imputed, un-normalized data
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3480
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3481 write.table(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3482 data_table_imputed
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3483 , file = imputed_data_filename
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3484 , sep = "\t"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3485 , 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
3486 , 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
3487 , quote = FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3488 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3489
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3490
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3491 #output quantile normalized data
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3492 impish <- cbind(rownames(quant_data_imp_qn_log), 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
3493 colnames(impish)[1] <- "Phosphopeptide"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3494 data_table_imputed <- sqldf(data_table_imputed_sql)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3495 # Zap the duplicated 'Phosphopeptide' column named 'ppep'
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3496 data_table_imputed <-
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3497 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))]
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3498 write.table(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3499 data_table_imputed,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3500 file = imp_qn_lt_data_filenm,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3501 sep = "\t",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3502 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
3503 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
3504 quote = FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3505 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3506
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3507 ppep_kinase <- sqldf("
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3508 SELECT DISTINCT k.ppep, k.kinase
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3509 FROM (
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3510 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3511 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
3512 WHERE GENE IN (SELECT kinase FROM enriched_kinases)
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3513 ) k
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3514 ORDER BY k.ppep, k.kinase
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3515 ")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3516
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3517 RSQLite::dbWriteTable(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3518 conn = db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3519 name = "ksea_enriched_ks",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3520 value = ppep_kinase,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3521 append = FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3522 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3523
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3524 RSQLite::dbWriteTable(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3525 conn = db,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3526 name = "anova_signif",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3527 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
3528 append = FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3529 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3530
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3531 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
3532 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
3533 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3534 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3535 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
3536 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
3537 AS
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3538 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
3539 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
3540 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
3541 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
3542 FROM
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3543 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
3544 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
3545 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
3546 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
3547 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
3548 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3549 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3550 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3551
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3552 write.table(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3553 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
3554 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
3555 sep = "\t",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3556 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
3557 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
3558 quote = FALSE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3559 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3560
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3561
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3562 ```
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3563
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3564 ```{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
3565 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
3566
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3567 # write parameters to report
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3568
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3569 param_unlist <- unlist(as.list(params))
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3570 param_df <- data.frame(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3571 parameter = paste0("\\verb@", names(param_unlist), "@"),
24
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3572 value = paste0(
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3573 "\n\\begin{tiny}\n\\verb@",
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3574 gsub("$", "\\$", param_unlist, fixed = TRUE),
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3575 "@\n\\end{tiny}"
8582a9797c18 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit c9e47049958ea3b12e30b9bd8884d48147c45edd
eschen42
parents: 22
diff changeset
3576 )
22
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3577 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3578
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3579 data_frame_latex(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3580 x = param_df,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3581 justification = "p{0.35\\linewidth} p{0.6\\linewidth}",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
parents: 15
diff changeset
3582 centered = TRUE,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
eschen42
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diff changeset
3583 caption = "Input parameters",
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diff changeset
3584 anchor = const_table_anchor_bp,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3585 underscore_whack = FALSE
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diff changeset
3586 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3587
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3588 # write parameters to SQLite output
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3589
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3590 mqppep_anova_script_param_df <- 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
3591 script = "mqppep_anova_script.Rmd",
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3592 parameter = names(param_unlist),
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3593 value = param_unlist
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3594 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3595 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3596 DROP TABLE IF EXISTS script_parameter;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3597 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3598 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3599 ddl_exec(db, "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3600 CREATE TABLE IF NOT EXISTS script_parameter(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3601 script TEXT,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3602 parameter TEXT,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3603 value ANY,
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3604 UNIQUE (script, parameter) ON CONFLICT REPLACE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3605 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3606 ;
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3607 "
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3608 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3609 RSQLite::dbWriteTable(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3610 conn = db,
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diff changeset
3611 name = "script_parameter",
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diff changeset
3612 value = mqppep_anova_script_param_df,
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diff changeset
3613 append = TRUE
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3614 )
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diff changeset
3615
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3616 # We are done with output
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diff changeset
3617 RSQLite::dbDisconnect(db)
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diff changeset
3618 ```
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3619 <!--
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3620 There's gotta be a better way...
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diff changeset
3621
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diff changeset
3622 loaded_packages_df <- sessioninfo::package_info("loaded")
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3623 loaded_packages_df[, "library"] <- as.character(loaded_packages_df$library)
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diff changeset
3624 loaded_packages_df <- data.frame(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3625 package = loaded_packages_df$package,
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diff changeset
3626 version = loaded_packages_df$loadedversion,
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diff changeset
3627 date = loaded_packages_df$date
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diff changeset
3628 )
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diff changeset
3629 data_frame_latex(
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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diff changeset
3630 x = loaded_packages_df,
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diff changeset
3631 justification = "l | l l",
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diff changeset
3632 centered = FALSE,
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diff changeset
3633 caption = "Loaded R packages",
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diff changeset
3634 anchor = const_table_anchor_bp
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diff changeset
3635 )
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
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3636 -->