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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2f3f29dbaaa8568b40818d3476159c384f1a21d6-dirty"
author eschen42
date Fri, 12 Feb 2021 18:05:29 +0000
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ae9ef9219aae "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2f3f29dbaaa8568b40818d3476159c384f1a21d6-dirty"
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1 #@authors ABiMS TEAM, Y. Guitton
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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3
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4 #@author G. Le Corguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
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6 parseCommandArgs <- function(...) {
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7 args <- batch::parseCommandArgs(...)
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8 for (key in names(args)) {
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9 if (args[key] %in% c("TRUE","FALSE"))
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10 args[key] = as.logical(args[key])
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11 }
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12 return(args)
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13 }
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15 #@author G. Le Corguille
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16 # This function will
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17 # - load the packages
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18 # - display the sessionInfo
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19 loadAndDisplayPackages <- function(pkgs) {
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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21
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22 sessioninfo = sessionInfo()
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23 cat(sessioninfo$R.version$version.string,"\n")
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24 cat("Main packages:\n")
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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26 cat("Other loaded packages:\n")
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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28 }
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29
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30 #@author G. Le Corguille
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31 # This function merge several chromBPI or chromTIC into one.
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32 mergeChrom <- function(chrom_merged, chrom) {
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33 if (is.null(chrom_merged)) return(NULL)
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
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35 return(chrom_merged)
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36 }
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38 #@author G. Le Corguille
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39 # This function merge several xdata into one.
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40 mergeXData <- function(args) {
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41 chromTIC <- NULL
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42 chromBPI <- NULL
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43 chromTIC_adjusted <- NULL
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44 chromBPI_adjusted <- NULL
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45 md5sumList <- NULL
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46 for(image in args$images) {
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47
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48 load(image)
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49 # Handle infiles
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50 if (!exists("singlefile")) singlefile <- NULL
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51 if (!exists("zipfile")) zipfile <- NULL
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52 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
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53 zipfile <- rawFilePath$zipfile
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54 singlefile <- rawFilePath$singlefile
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55
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56 if (exists("raw_data")) xdata <- raw_data
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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58
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59 cat(sampleNamesList$sampleNamesOrigin,"\n")
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60
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61 if (!exists("xdata_merged")) {
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62 xdata_merged <- xdata
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63 singlefile_merged <- singlefile
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64 md5sumList_merged <- md5sumList
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65 sampleNamesList_merged <- sampleNamesList
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66 chromTIC_merged <- chromTIC
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67 chromBPI_merged <- chromBPI
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68 chromTIC_adjusted_merged <- chromTIC_adjusted
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69 chromBPI_adjusted_merged <- chromBPI_adjusted
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70 } else {
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata)
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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74
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75 singlefile_merged <- c(singlefile_merged,singlefile)
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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83 }
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84 }
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85 rm(image)
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86 xdata <- xdata_merged; rm(xdata_merged)
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87 singlefile <- singlefile_merged; rm(singlefile_merged)
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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90
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91 if (!is.null(args$sampleMetadata)) {
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92 cat("\tXSET PHENODATA SETTING...\n")
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93 sampleMetadataFile <- args$sampleMetadata
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
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96
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97 if (any(is.na(pData(xdata)$sample_group))) {
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
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100 print(error_message)
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101 stop(error_message)
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102 }
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103 }
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104
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
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107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
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108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
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109
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110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
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111 }
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112
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113 #@author G. Le Corguille
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114 # This function convert if it is required the Retention Time in minutes
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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116 if (convertRTMinute){
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117 #converting the retention times (seconds) into minutes
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118 print("converting the retention times into minutes in the variableMetadata")
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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122 }
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123 return (variableMetadata)
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124 }
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125
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126 #@author G. Le Corguille
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127 # This function format ions identifiers
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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133 return(variableMetadata)
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134 }
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135
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136 #@author G. Le Corguille
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137 # This function convert the remain NA to 0 in the dataMatrix
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138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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139 if (naTOzero){
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140 dataMatrix[is.na(dataMatrix)] <- 0
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141 }
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142 return (dataMatrix)
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143 }
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144
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145 #@author G. Le Corguille
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146 # Draw the plotChromPeakDensity 3 per page in a pdf file
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147 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) {
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148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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149
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150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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151
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152 if(length(unique(xdata$sample_group))<10){
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153 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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154 }else{
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155 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
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156 }
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157 names(group_colors) <- unique(xdata$sample_group)
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158 col_per_samp <- as.character(xdata$sample_group)
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159 for(i in 1:length(group_colors)){col_per_samp[col_per_samp==(names(group_colors)[i])]<-group_colors[i]}
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160
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161 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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162 for (i in 1:nrow(featureDefinitions(xdata))) {
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163 mzmin = featureDefinitions(xdata)[i,]$mzmin
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164 mzmax = featureDefinitions(xdata)[i,]$mzmax
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165 plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=col_per_samp, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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166 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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167 }
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168
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169 dev.off()
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170 }
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171
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172 #@author G. Le Corguille
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173 # Draw the plotChromPeakDensity 3 per page in a pdf file
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174 getPlotAdjustedRtime <- function(xdata) {
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175
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176 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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177
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178 # Color by group
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179 if(length(unique(xdata$sample_group))<10){
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180 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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181 }else{
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182 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
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183 }
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184 if (length(group_colors) > 1) {
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185 names(group_colors) <- unique(xdata$sample_group)
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186 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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187 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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188 }
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189
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190 # Color by sample
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191 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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192 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
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193
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194 dev.off()
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195 }
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196
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197 #@author G. Le Corguille
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198 # value: intensity values to be used into, maxo or intb
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199 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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200 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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201 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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202 dataMatrix = cbind(name=groupnames(xdata), dataMatrix)
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203 variableMetadata <- featureDefinitions(xdata)
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204 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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205 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata)
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206
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207 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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208 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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209 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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210
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211 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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212 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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213
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214 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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215 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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216
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217 }
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218
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219 #@author G. Le Corguille
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220 # It allow different of field separators
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221 getDataFrameFromFile <- function(filename, header=T) {
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222 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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223 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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224 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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225 if (ncol(myDataFrame) < 2) {
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226 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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227 print(error_message)
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228 stop(error_message)
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229 }
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230 return(myDataFrame)
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231 }
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232
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233 #@author G. Le Corguille
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234 # Draw the BPI and TIC graphics
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235 # colored by sample names or class names
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236 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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237
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238 if (aggregationFun == "sum")
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239 type="Total Ion Chromatograms"
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240 else
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241 type="Base Peak Intensity Chromatograms"
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242
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243 adjusted="Raw"
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244 if (hasAdjustedRtime(xdata))
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245 adjusted="Adjusted"
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246
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247 main <- paste(type,":",adjusted,"data")
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248
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249 pdf(pdfname, width=16, height=10)
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250
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251 # Color by group
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252 if(length(unique(xdata$sample_group))<10){
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253 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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254 }else{
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255 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
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256 }
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257 if (length(group_colors) > 1) {
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258 names(group_colors) <- unique(xdata$sample_group)
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259 plot(chrom, col = group_colors[chrom$sample_group], main=main, peakType = "none")
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260 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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261 }
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262
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263 # Color by sample
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264 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main, peakType = "none")
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265 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
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266
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267 dev.off()
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268 }
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269
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270
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271 # Get the polarities from all the samples of a condition
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272 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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273 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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274 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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275 cat("Creating the sampleMetadata file...\n")
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276
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277 #Create the sampleMetada dataframe
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278 sampleMetadata <- xdata@phenoData@data
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279 rownames(sampleMetadata) <- NULL
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280 colnames(sampleMetadata) <- c("sample_name", "class")
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281
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282 sampleNamesOrigin <- sampleMetadata$sample_name
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283 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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284
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285 if (any(duplicated(sampleNamesMakeNames))) {
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286 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
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287 for (sampleName in sampleNamesOrigin) {
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288 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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289 }
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290 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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291 }
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292
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293 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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294 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
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295 for (sampleName in sampleNamesOrigin) {
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296 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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297 }
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298 }
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299
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300 sampleMetadata$sample_name <- sampleNamesMakeNames
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301
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302
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303 #For each sample file, the following actions are done
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304 for (fileIdx in 1:length(fileNames(xdata))) {
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305 #Check if the file is in the CDF format
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306 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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307
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308 # If the column isn't exist, with add one filled with NA
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309 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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310
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311 #Extract the polarity (a list of polarities)
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312 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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313 #Verify if all the scans have the same polarity
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314 uniq_list <- unique(polarity)
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315 if (length(uniq_list)>1){
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316 polarity <- "mixed"
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317 } else {
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318 polarity <- as.character(uniq_list)
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319 }
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320
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321 #Set the polarity attribute
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322 sampleMetadata$polarity[fileIdx] <- polarity
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323 }
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324
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325 }
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326
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327 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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328
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329 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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330
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331 }
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332
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333
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334 # This function will compute MD5 checksum to check the data integrity
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335 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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336 getMd5sum <- function (files) {
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337 cat("Compute md5 checksum...\n")
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338 library(tools)
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339 return(as.matrix(md5sum(files)))
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340 }
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341
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342 # This function retrieve the raw file in the working directory
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343 # - if zipfile: unzip the file with its directory tree
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344 # - if singlefiles: set symlink with the good filename
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345 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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346 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile, args, prefix="") {
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347
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348 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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349
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350 # single - if the file are passed in the command arguments -> refresh singlefile
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351 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
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352 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath",prefix)]],"\\|"))
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353 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName",prefix)]],"\\|"))
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354
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355 singlefile <- NULL
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356 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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357 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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358 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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359 # In case, an url is used to import data within Galaxy
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360 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
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361 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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362 }
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363 }
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364 # zipfile - if the file are passed in the command arguments -> refresh zipfile
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365 if (!is.null(args[[paste0("zipfile",prefix)]]))
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366 zipfile <- args[[paste0("zipfile",prefix)]]
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367
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368 # single
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369 if(!is.null(singlefile) && (length("singlefile")>0)) {
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370 files <- vector()
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371 for (singlefile_sampleName in names(singlefile)) {
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372 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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373 if(!file.exists(singlefile_galaxyPath)){
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374 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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375 print(error_message); stop(error_message)
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376 }
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377
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378 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
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379 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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380 files <- c(files, singlefile_sampleName)
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381 }
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382 }
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383 # zipfile
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384 if(!is.null(zipfile) && (zipfile != "")) {
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385 if(!file.exists(zipfile)){
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386 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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387 print(error_message)
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388 stop(error_message)
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389 }
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390 suppressWarnings(unzip(zipfile, unzip="unzip"))
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391
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392 #get the directory name
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393 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
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394 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
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395 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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396 directory <- "."
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397 if (length(directories) == 1) directory <- directories
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398
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399 cat("files_root_directory\t",directory,"\n")
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400
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401 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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402 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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403 info <- file.info(directory)
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404 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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405 files <- c(directory[!info$isdir], listed)
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406 exists <- file.exists(files)
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407 files <- files[exists]
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408
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409 }
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410 return(list(zipfile=zipfile, singlefile=singlefile, files=files))
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411
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diff changeset
412 }
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parents:
diff changeset
413
ae9ef9219aae "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2f3f29dbaaa8568b40818d3476159c384f1a21d6-dirty"
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diff changeset
414
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415 # This function retrieve a xset like object
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416 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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417 getxcmsSetObject <- function(xobject) {
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418 # XCMS 1.x
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419 if (class(xobject) == "xcmsSet")
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420 return (xobject)
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421 # XCMS 3.x
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422 if (class(xobject) == "XCMSnExp") {
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423 # Get the legacy xcmsSet object
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424 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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diff changeset
425 if (!is.null(xset@phenoData$sample_group))
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426 sampclass(xset) <- xset@phenoData$sample_group
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diff changeset
427 else
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428 sampclass(xset) <- "."
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diff changeset
429 return (xset)
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430 }
ae9ef9219aae "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2f3f29dbaaa8568b40818d3476159c384f1a21d6-dirty"
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431 }