Mercurial > repos > tomnl > mspurity_flagremove

annotate purityX.R @ 1:a03407367135 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e67cf7a95ce430d1d373c03992a615da2f3eeeb1
author tomnl
date Tue, 04 Jun 2019 10:48:33 -0400
parents ca0ac330f1a4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ca0ac330f1a4 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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1 library(msPurity)
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2 library(optparse)
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3 print(sessionInfo())
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5 option_list <- list(
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6 make_option(c("--xset_path"), type="character"),
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7 make_option(c("-o", "--out_dir"), type="character"),
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8 make_option(c("--mzML_path"), type="character"),
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9 make_option("--minOffset", default=0.5),
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10 make_option("--maxOffset", default=0.5),
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11 make_option("--ilim", default=0.05),
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12 make_option("--iwNorm", default="none", type="character"),
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13 make_option("--exclude_isotopes", action="store_true"),
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14 make_option("--isotope_matrix", type="character"),
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15 make_option("--purityType", default="purityFWHMmedian"),
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16 make_option("--singleFile", default=0),
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17 make_option("--cores", default=4),
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18 make_option("--xgroups", type="character"),
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19 make_option("--rdata_name", default='xset'),
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20 make_option("--camera_xcms", default='xset'),
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21 make_option("--files", type="character"),
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22 make_option("--galaxy_files", type="character"),
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23 make_option("--choose_class", type="character"),
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24 make_option("--ignore_files", type="character"),
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25 make_option("--rtraw_columns", action="store_true")
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26 )
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29 opt<- parse_args(OptionParser(option_list=option_list))
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30 print(opt)
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33 if (!is.null(opt$xgroups)){
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34 xgroups = as.numeric(strsplit(opt$xgroups, ',')[[1]])
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35 }else{
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36 xgroups = NULL
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37 }
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41 print(xgroups)
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43 if (!is.null(opt$remove_nas)){
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44 df <- df[!is.na(df$mz),]
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45 }
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47 if (is.null(opt$isotope_matrix)){
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48 im <- NULL
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49 }else{
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50 im <- read.table(opt$isotope_matrix,
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51 header = TRUE, sep='\t', stringsAsFactors = FALSE)
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52 }
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53
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54 if (is.null(opt$exclude_isotopes)){
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55 isotopes <- FALSE
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56 }else{
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57 isotopes <- TRUE
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58 }
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59
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60 if (is.null(opt$rtraw_columns)){
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61 rtraw_columns <- FALSE
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62 }else{
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63 rtraw_columns <- TRUE
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64 }
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65
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66 loadRData <- function(rdata_path, xset_name){
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67 #loads an RData file, and returns the named xset object if it is there
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68 load(rdata_path)
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69 return(get(ls()[ls() == xset_name]))
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70 }
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71
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72 target_obj <- loadRData(opt$xset_path, opt$rdata_name)
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74 if (opt$camera_xcms=='camera'){
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75 xset <- target_obj@xcmsSet
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76 }else{
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77 xset <- target_obj
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78 }
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79
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80 print(xset)
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81
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82 minOffset = as.numeric(opt$minOffset)
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83 maxOffset = as.numeric(opt$maxOffset)
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84
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85
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86 if (opt$iwNorm=='none'){
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87 iwNorm = FALSE
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88 iwNormFun = NULL
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89 }else if (opt$iwNorm=='gauss'){
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90 iwNorm = TRUE
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91 iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset)
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92 }else if (opt$iwNorm=='rcosine'){
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93 iwNorm = TRUE
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94 iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset)
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95 }else if (opt$iwNorm=='QE5'){
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96 iwNorm = TRUE
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97 iwNormFun = msPurity::iwNormQE.5()
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98 }
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99
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100 print(xset@filepaths)
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101
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102 if (!is.null(opt$files)){
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103 updated_filepaths <- trimws(strsplit(opt$files, ',')[[1]])
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104 updated_filepaths <- updated_filepaths[updated_filepaths != ""]
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105 print(updated_filepaths)
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106 updated_filenames = basename(updated_filepaths)
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107 original_filenames = basename(xset@filepaths)
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108 update_idx = match(updated_filenames, original_filenames)
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109
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110 if (!is.null(opt$galaxy_files)){
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111 galaxy_files <- trimws(strsplit(opt$galaxy_files, ',')[[1]])
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112 galaxy_files <- galaxy_files[galaxy_files != ""]
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113 xset@filepaths <- galaxy_files[update_idx]
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114 }else{
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115 xset@filepaths <- updated_filepaths[update_idx]
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116 }
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117 }
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118
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119 if (!is.null(opt$choose_class)){
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120 classes <- trimws(strsplit(opt$choose_class, ',')[[1]])
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121
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122
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123 ignore_files_class <- which(!as.character(xset@phenoData$class) %in% classes)
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124
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125 print('choose class')
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126 print(ignore_files_class)
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127 }else{
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128 ignore_files_class <- NA
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129 }
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130
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131 if (!is.null(opt$ignore_files)){
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132 ignore_files_string <- trimws(strsplit(opt$ignore_files, ',')[[1]])
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133 filenames <- rownames(xset@phenoData)
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134 ignore_files <- which(filenames %in% ignore_files_string)
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135
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136 ignore_files <- unique(c(ignore_files, ignore_files_class))
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137 ignore_files <- ignore_files[ignore_files != ""]
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138 }else{
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139 if (anyNA(ignore_files_class)){
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140 ignore_files <- NULL
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141 }else{
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142 ignore_files <- ignore_files_class
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143 }
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144
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145 }
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146
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147 print('ignore_files')
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148 print(ignore_files)
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149
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150
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151 ppLCMS <- msPurity::purityX(xset=xset,
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152 offsets=c(minOffset, maxOffset),
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153 cores=opt$cores,
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154 xgroups=xgroups,
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155 purityType=opt$purityType,
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156 ilim = opt$ilim,
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157 isotopes = isotopes,
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158 im = im,
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159 iwNorm = iwNorm,
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160 iwNormFun = iwNormFun,
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161 singleFile = opt$singleFile,
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162 fileignore = ignore_files,
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163 rtrawColumns=rtraw_columns)
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164
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165
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166 dfp <- ppLCMS@predictions
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167
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168 # to make compatable with deconrank
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169 colnames(dfp)[colnames(dfp)=='grpid'] = 'peakID'
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170 colnames(dfp)[colnames(dfp)=='median'] = 'medianPurity'
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171 colnames(dfp)[colnames(dfp)=='mean'] = 'meanPurity'
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172 colnames(dfp)[colnames(dfp)=='sd'] = 'sdPurity'
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173 colnames(dfp)[colnames(dfp)=='stde'] = 'sdePurity'
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174 colnames(dfp)[colnames(dfp)=='RSD'] = 'cvPurity'
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175 colnames(dfp)[colnames(dfp)=='pknm'] = 'pknmPurity'
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176 if(sum(is.na(dfp$medianPurity))>0){
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177 dfp[is.na(dfp$medianPurity),]$medianPurity = 0
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178 }
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179
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180
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181 print(head(dfp))
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182 write.table(dfp, file.path(opt$out_dir, 'purityX_output.tsv'), row.names=FALSE, sep='\t')
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183
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184 save.image(file.path(opt$out_dir, 'purityX_output.RData'))