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annotate lib.r @ 23:dcff3c4a8c80 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5583baab62c0f17cabbfe93ba4f2522e8df9b36b
author lecorguille
date Thu, 30 Mar 2017 08:34:09 -0400
parents a79d839d625f
children 36b470f3ebcf
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1 #Authors ABiMS TEAM
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2 #Lib.r for Galaxy Workflow4Metabolomics xcms tools
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3 #
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4 #version 2.4: lecorguille
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5 # add getPeaklistW4M
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6 #version 2.3: yguitton
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7 # correction for empty PDF when only 1 class
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8 #version 2.2
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9 # correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet
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10 # Note if scanrange is used a warning is prompted in R console but do not stop PDF generation
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11 #version 2.1: yguitton
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12 # Modifications made by Guitton Yann
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15 #@author G. Le Corguille
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16 #This function convert if it is required the Retention Time in minutes
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17 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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18 if (convertRTMinute){
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19 #converting the retention times (seconds) into minutes
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20 print("converting the retention times into minutes in the variableMetadata")
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21 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60
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22 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60
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23 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60
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24 }
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25 return (variableMetadata)
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26 }
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28 #@author G. Le Corguille
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29 #This function format ions identifiers
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30 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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31 splitDeco = strsplit(as.character(variableMetadata$name),"_")
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32 idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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33 namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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34 variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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35 return(variableMetadata)
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36 }
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38 #@author G. Le Corguille
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39 # value: intensity values to be used into, maxo or intb
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40 getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) {
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41 variableMetadata_dataMatrix = peakTable(xset, method="medret", value=intval)
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42 variableMetadata_dataMatrix = cbind(name=groupnames(xset),variableMetadata_dataMatrix)
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44 dataMatrix = variableMetadata_dataMatrix[,(make.names(colnames(variableMetadata_dataMatrix)) %in% c("name", make.names(sampnames(xset))))]
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46 variableMetadata = variableMetadata_dataMatrix[,!(make.names(colnames(variableMetadata_dataMatrix)) %in% c(make.names(sampnames(xset))))]
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47 variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)
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48 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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49
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50 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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51 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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52 }
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54 #@author Y. Guitton
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55 getBPC <- function(file,rtcor=NULL, ...) {
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56 object <- xcmsRaw(file)
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57 sel <- profRange(object, ...)
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58 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
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59 #plotChrom(xcmsRaw(file), base=T)
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60 }
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62 #@author Y. Guitton
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63 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
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64 cat("Creating BIC pdf...\n")
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65
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66 if (is.null(xcmsSet)) {
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67 cat("Enter an xcmsSet \n")
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68 stop()
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69 } else {
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70 files <- filepaths(xcmsSet)
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71 }
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72
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73 phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
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75 classnames<-vector("list",length(phenoDataClass))
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76 for (i in 1:length(phenoDataClass)){
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77 classnames[[i]]<-which( xcmsSet@phenoData[,1]==phenoDataClass[i])
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78 }
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79
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80 N <- dim(phenoData(xcmsSet))[1]
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81
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82 TIC <- vector("list",N)
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85 for (j in 1:N) {
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86
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87 TIC[[j]] <- getBPC(files[j])
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88 #good for raw
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89 # seems strange for corrected
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90 #errors if scanrange used in xcmsSetgeneration
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91 if (!is.null(xcmsSet) && rt == "corrected")
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92 rtcor <- xcmsSet@rt$corrected[[j]]
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93 else
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94 rtcor <- NULL
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95
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96 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
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97 # TIC[[j]][,1]<-rtcor
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98 }
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99
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100
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101
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102 pdf(pdfname,w=16,h=10)
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103 cols <- rainbow(N)
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104 lty = 1:N
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105 pch = 1:N
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106 #search for max x and max y in BPCs
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107 xlim = range(sapply(TIC, function(x) range(x[,1])))
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108 ylim = range(sapply(TIC, function(x) range(x[,2])))
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109 ylim = c(-ylim[2], ylim[2])
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110
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111
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112 ##plot start
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113
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114 if (length(phenoDataClass)>2){
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115 for (k in 1:(length(phenoDataClass)-1)){
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116 for (l in (k+1):length(phenoDataClass)){
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117 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
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118 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
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119 colvect<-NULL
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120 for (j in 1:length(classnames[[k]])) {
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121 tic <- TIC[[classnames[[k]][j]]]
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122 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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123 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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124 colvect<-append(colvect,cols[classnames[[k]][j]])
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125 }
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126 for (j in 1:length(classnames[[l]])) {
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127 # i=class2names[j]
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128 tic <- TIC[[classnames[[l]][j]]]
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129 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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130 colvect<-append(colvect,cols[classnames[[l]][j]])
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131 }
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132 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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133 }
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134 }
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135 }#end if length >2
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136
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137 if (length(phenoDataClass)==2){
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138 k=1
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139 l=2
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140 colvect<-NULL
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141 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
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142
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143 for (j in 1:length(classnames[[k]])) {
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144
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145 tic <- TIC[[classnames[[k]][j]]]
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146 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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147 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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148 colvect<-append(colvect,cols[classnames[[k]][j]])
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149 }
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150 for (j in 1:length(classnames[[l]])) {
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151 # i=class2names[j]
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152 tic <- TIC[[classnames[[l]][j]]]
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153 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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154 colvect<-append(colvect,cols[classnames[[l]][j]])
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155 }
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156 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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157
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158 }#end length ==2
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159
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160 #case where only one class
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161 if (length(phenoDataClass)==1){
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162 k=1
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163 ylim = range(sapply(TIC, function(x) range(x[,2])))
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164 colvect<-NULL
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165 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
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166
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167 for (j in 1:length(classnames[[k]])) {
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168 tic <- TIC[[classnames[[k]][j]]]
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169 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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170 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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171 colvect<-append(colvect,cols[classnames[[k]][j]])
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172 }
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173
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174 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
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175
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176 }#end length ==1
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177
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178 dev.off() #pdf(pdfname,w=16,h=10)
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179
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180 invisible(TIC)
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181 }
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182
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183
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184
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185 #@author Y. Guitton
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186 getTIC <- function(file,rtcor=NULL) {
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187 object <- xcmsRaw(file)
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188 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity)
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189 }
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190
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191 ##
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192 ## overlay TIC from all files in current folder or from xcmsSet, create pdf
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193 ##
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194 #@author Y. Guitton
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195 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) {
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196 cat("Creating TIC pdf...\n")
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197
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198 if (is.null(xcmsSet)) {
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199 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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200 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
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201 if (is.null(files))
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202 files <- getwd()
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203 info <- file.info(files)
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204 listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
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205 files <- c(files[!info$isdir], listed)
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206 } else {
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207 files <- filepaths(xcmsSet)
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208 }
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209
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210 phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
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211 classnames<-vector("list",length(phenoDataClass))
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212 for (i in 1:length(phenoDataClass)){
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213 classnames[[i]]<-which( xcmsSet@phenoData[,1]==phenoDataClass[i])
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214 }
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215
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216 N <- length(files)
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217 TIC <- vector("list",N)
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218
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219 for (i in 1:N) {
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220 if (!is.null(xcmsSet) && rt == "corrected")
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221 rtcor <- xcmsSet@rt$corrected[[i]] else
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222 rtcor <- NULL
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223 TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
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224 }
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225
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226 pdf(pdfname,w=16,h=10)
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227 cols <- rainbow(N)
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228 lty = 1:N
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229 pch = 1:N
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230 #search for max x and max y in TICs
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231 xlim = range(sapply(TIC, function(x) range(x[,1])))
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232 ylim = range(sapply(TIC, function(x) range(x[,2])))
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233 ylim = c(-ylim[2], ylim[2])
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234
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235
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236 ##plot start
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237 if (length(phenoDataClass)>2){
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238 for (k in 1:(length(phenoDataClass)-1)){
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239 for (l in (k+1):length(phenoDataClass)){
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240 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
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241 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
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242 colvect<-NULL
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243 for (j in 1:length(classnames[[k]])) {
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244 tic <- TIC[[classnames[[k]][j]]]
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245 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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246 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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247 colvect<-append(colvect,cols[classnames[[k]][j]])
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248 }
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249 for (j in 1:length(classnames[[l]])) {
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250 # i=class2names[j]
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251 tic <- TIC[[classnames[[l]][j]]]
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252 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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253 colvect<-append(colvect,cols[classnames[[l]][j]])
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254 }
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255 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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256 }
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257 }
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258 }#end if length >2
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259 if (length(phenoDataClass)==2){
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260 k=1
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261 l=2
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262
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263 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
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264 colvect<-NULL
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265 for (j in 1:length(classnames[[k]])) {
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266 tic <- TIC[[classnames[[k]][j]]]
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267 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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268 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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269 colvect<-append(colvect,cols[classnames[[k]][j]])
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270 }
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271 for (j in 1:length(classnames[[l]])) {
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272 # i=class2names[j]
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273 tic <- TIC[[classnames[[l]][j]]]
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274 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
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275 colvect<-append(colvect,cols[classnames[[l]][j]])
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276 }
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277 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
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278
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279 }#end length ==2
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280
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281 #case where only one class
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282 if (length(phenoDataClass)==1){
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283 k=1
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284 ylim = range(sapply(TIC, function(x) range(x[,2])))
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285
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286 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
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287 colvect<-NULL
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288 for (j in 1:length(classnames[[k]])) {
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289 tic <- TIC[[classnames[[k]][j]]]
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290 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
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291 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
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292 colvect<-append(colvect,cols[classnames[[k]][j]])
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293 }
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294
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295 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
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296
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297 }#end length ==1
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298
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299 dev.off() #pdf(pdfname,w=16,h=10)
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300
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301 invisible(TIC)
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302 }
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303
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304
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305
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306 ##
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307 ## Get the polarities from all the samples of a condition
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308 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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309 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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310 getSampleMetadata <- function(xcmsSet=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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311 cat("Creating the sampleMetadata file...\n")
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312
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313 #Create the sampleMetada dataframe
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314 sampleMetadata=xset@phenoData
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315 sampleNamesOrigin=rownames(sampleMetadata)
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316 sampleNamesMakeNames=make.names(sampleNamesOrigin)
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317
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318 if (any(duplicated(sampleNamesMakeNames))) {
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319 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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320 for (sampleName in sampleNamesOrigin) {
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321 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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322 }
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323 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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324 }
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325
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326 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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327 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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328 for (sampleName in sampleNamesOrigin) {
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329 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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330 }
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331 }
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332
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333 sampleMetadata$sampleMetadata=sampleNamesMakeNames
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334 sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns
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335 rownames(sampleMetadata)=NULL
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336
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337 #Create a list of files name in the current directory
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338 list_files=xset@filepaths
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339 #For each sample file, the following actions are done
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340 for (file in list_files){
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341 #Check if the file is in the CDF format
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342 if (!mzR:::netCDFIsFile(file)){
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343
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344 # If the column isn't exist, with add one filled with NA
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345 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA
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346
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347 #Create a simple xcmsRaw object for each sample
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348 xcmsRaw=xcmsRaw(file)
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349 #Extract the polarity (a list of polarities)
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350 polarity=xcmsRaw@polarity
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351 #Verify if all the scans have the same polarity
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352 uniq_list=unique(polarity)
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353 if (length(uniq_list)>1){
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354 polarity="mixed"
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355 } else {
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356 polarity=as.character(uniq_list)
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357 }
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358 #Transforms the character to obtain only the sample name
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359 filename=basename(file)
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360 library(tools)
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361 samplename=file_path_sans_ext(filename)
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362
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363 #Set the polarity attribute
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364 sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity
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365
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366 #Delete xcmsRaw object because it creates a bug for the fillpeaks step
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367 rm(xcmsRaw)
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368 }
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369
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370 }
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371
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372 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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373
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374 return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames))
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375
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376 }
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377
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378
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379 ##
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380 ## This function check if xcms will found all the files
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381 ##
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382 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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383 checkFilesCompatibilityWithXcms <- function(directory) {
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384 cat("Checking files filenames compatibilities with xmcs...\n")
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385 # WHAT XCMS WILL FIND
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386 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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387 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
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388 info <- file.info(directory)
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389 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
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390 files <- c(directory[!info$isdir], listed)
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391 files_abs <- file.path(getwd(), files)
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392 exists <- file.exists(files_abs)
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393 files[exists] <- files_abs[exists]
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394 files[exists] <- sub("//","/",files[exists])
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395
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396 # WHAT IS ON THE FILESYSTEM
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397 filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
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398 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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399
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400 # COMPARISON
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401 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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402 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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403 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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404 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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405 }
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406 }
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407
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408
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409
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410 ##
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411 ## This function check if XML contains special caracters. It also checks integrity and completness.
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412 ##
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413 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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414 checkXmlStructure <- function (directory) {
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415 cat("Checking XML structure...\n")
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416
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417 cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
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418 capture=system(cmd,intern=TRUE)
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419
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420 if (length(capture)>0){
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421 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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422 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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423 write(capture, stderr())
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424 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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425 }
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426
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427 }
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428
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429
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430 ##
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431 ## This function check if XML contain special characters
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432 ##
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433 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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434 deleteXmlBadCharacters<- function (directory) {
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435 cat("Checking Non ASCII characters in the XML...\n")
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436
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437 processed=F
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438 l=system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"),intern=TRUE)
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439 for (i in l){
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440 cmd=paste("LC_ALL=C grep '[^ -~]' \"",i,"\"",sep="")
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441 capture=suppressWarnings(system(cmd,intern=TRUE))
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442 if (length(capture)>0){
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443 cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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444 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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445 c=system(cmd,intern=TRUE)
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446 capture=""
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447 processed=T
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448 }
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449 }
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450 if (processed) cat("\n\n")
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451 return(processed)
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452 }
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453
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454
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455 ##
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456 ## This function will compute MD5 checksum to check the data integrity
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457 ##
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458 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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459 getMd5sum <- function (directory) {
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460 cat("Compute md5 checksum...\n")
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461 # WHAT XCMS WILL FIND
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462 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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463 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
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464 info <- file.info(directory)
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465 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
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466 files <- c(directory[!info$isdir], listed)
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467 exists <- file.exists(files)
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468 files <- files[exists]
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469
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470 library(tools)
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471
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472 #cat("\n\n")
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473
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474 return(as.matrix(md5sum(files)))
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475 }
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476
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477
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478 # This function get the raw file path from the arguments
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479 getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {
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480 if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]]
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481 if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]]
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482 if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]]
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483
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484 if (!is.null(listArguments[["singlefile_galaxyPath"]])) {
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485 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]];
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
486 singlefile_sampleNames = listArguments[["singlefile_sampleName"]]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
487 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
488 if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
489 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]];
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
490 singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
491 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
492 if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
493 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]];
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
494 singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
495 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
496 if (exists("singlefile_galaxyPaths")){
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
497 singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
498 singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
499
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
500 singlefile=NULL
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
501 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
502 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
503 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
504 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
505 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
506 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
507 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
508 listArguments[[argument]]=NULL
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
509 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
510 return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments))
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
511 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
512
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
513
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
514 # This function retrieve the raw file in the working directory
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
515 # - if zipfile: unzip the file with its directory tree
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
516 # - if singlefiles: set symlink with the good filename
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
517 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
518 if(!is.null(singlefile) && (length("singlefile")>0)) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
519 for (singlefile_sampleName in names(singlefile)) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
520 singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
521 if(!file.exists(singlefile_galaxyPath)){
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
522 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
523 print(error_message); stop(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
524 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
525
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
526 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
527 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
528 directory = "."
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
529
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
530 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
531 if(!is.null(zipfile) && (zipfile!="")) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
532 if(!file.exists(zipfile)){
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
533 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
534 print(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
535 stop(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
536 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
537
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
538 #list all file in the zip file
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
539 #zip_files=unzip(zipfile,list=T)[,"Name"]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
540
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
541 #unzip
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
542 suppressWarnings(unzip(zipfile, unzip="unzip"))
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
543
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
544 #get the directory name
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
545 filesInZip=unzip(zipfile, list=T);
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
546 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
547 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
548 directory = "."
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
549 if (length(directories) == 1) directory = directories
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
550
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
551 cat("files_root_directory\t",directory,"\n")
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
552
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
553 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
554 return (directory)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
555 }