annotate lib.r @ 15:950b97b679c6 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
author lecorguille
date Mon, 11 Feb 2019 06:06:50 -0500
parents e95f0dcdea3b
children 0dcc9d0902cf
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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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14
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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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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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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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37
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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 for(image in args$images) {
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47 load(image)
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48 # Handle infiles
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49 if (!exists("singlefile")) singlefile <- NULL
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50 if (!exists("zipfile")) zipfile <- NULL
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51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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52 zipfile <- rawFilePath$zipfile
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53 singlefile <- rawFilePath$singlefile
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54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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55
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56 if (exists("raw_data")) xdata <- raw_data
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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58
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59 cat(sampleNamesList$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 <- .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 }
2
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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 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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153 names(group_colors) <- unique(xdata$sample_group)
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154
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155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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156 for (i in 1:nrow(featureDefinitions(xdata))) {
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157 mzmin = featureDefinitions(xdata)[i,]$mzmin
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158 mzmax = featureDefinitions(xdata)[i,]$mzmax
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159 plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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161 }
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162
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163 dev.off()
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164 }
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165
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166 #@author G. Le Corguille
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167 # Draw the plotChromPeakDensity 3 per page in a pdf file
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168 getPlotAdjustedRtime <- function(xdata) {
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169
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170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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171
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172 # Color by group
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173 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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174 if (length(group_colors) > 1) {
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175 names(group_colors) <- unique(xdata$sample_group)
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176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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178 }
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179
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180 # Color by sample
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181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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182 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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183
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184 dev.off()
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185 }
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186
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187 #@author G. Le Corguille
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188 # value: intensity values to be used into, maxo or intb
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189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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192 dataMatrix = cbind(name=groupnames(xdata), dataMatrix)
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193 variableMetadata <- featureDefinitions(xdata)
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194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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195 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata)
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196
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197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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200
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201 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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202 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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203
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204 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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205 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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206
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207 }
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208
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209 #@author G. Le Corguille
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210 # It allow different of field separators
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211 getDataFrameFromFile <- function(filename, header=T) {
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212 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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213 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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214 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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215 if (ncol(myDataFrame) < 2) {
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216 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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217 print(error_message)
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218 stop(error_message)
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219 }
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220 return(myDataFrame)
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221 }
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222
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223 #@author G. Le Corguille
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224 # Draw the BPI and TIC graphics
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225 # colored by sample names or class names
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226 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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227
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228 if (aggregationFun == "sum")
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229 type="Total Ion Chromatograms"
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230 else
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231 type="Base Peak Intensity Chromatograms"
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232
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233 adjusted="Raw"
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234 if (hasAdjustedRtime(xdata))
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235 adjusted="Adjusted"
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236
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237 main <- paste(type,":",adjusted,"data")
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238
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239 pdf(pdfname, width=16, height=10)
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240
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241 # Color by group
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242 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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243 if (length(group_colors) > 1) {
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244 names(group_colors) <- unique(xdata$sample_group)
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245 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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246 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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247 }
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248
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249 # Color by sample
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250 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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251 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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252
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253 dev.off()
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254 }
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255
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256
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257 # Get the polarities from all the samples of a condition
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258 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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259 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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260 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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261 cat("Creating the sampleMetadata file...\n")
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262
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263 #Create the sampleMetada dataframe
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264 sampleMetadata <- xdata@phenoData@data
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265 rownames(sampleMetadata) <- NULL
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266 colnames(sampleMetadata) <- c("sample_name", "class")
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267
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268 sampleNamesOrigin <- sampleMetadata$sample_name
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269 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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270
8
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271 if (any(duplicated(sampleNamesMakeNames))) {
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272 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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273 for (sampleName in sampleNamesOrigin) {
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274 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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275 }
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276 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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277 }
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278
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279 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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280 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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281 for (sampleName in sampleNamesOrigin) {
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282 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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283 }
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284 }
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285
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286 sampleMetadata$sample_name <- sampleNamesMakeNames
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287
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288
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289 #For each sample file, the following actions are done
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290 for (fileIdx in 1:length(fileNames(xdata))) {
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291 #Check if the file is in the CDF format
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292 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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293
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294 # If the column isn't exist, with add one filled with NA
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295 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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296
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297 #Extract the polarity (a list of polarities)
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298 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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299 #Verify if all the scans have the same polarity
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300 uniq_list <- unique(polarity)
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301 if (length(uniq_list)>1){
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302 polarity <- "mixed"
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303 } else {
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304 polarity <- as.character(uniq_list)
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305 }
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306
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307 #Set the polarity attribute
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308 sampleMetadata$polarity[fileIdx] <- polarity
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309 }
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310
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311 }
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312
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313 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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314
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315 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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316
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317 }
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318
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319
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320 # This function check if xcms will found all the files
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321 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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322 checkFilesCompatibilityWithXcms <- function(directory) {
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323 cat("Checking files filenames compatibilities with xmcs...\n")
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324 # WHAT XCMS WILL FIND
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325 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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326 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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327 info <- file.info(directory)
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328 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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329 files <- c(directory[!info$isdir], listed)
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330 files_abs <- file.path(getwd(), files)
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331 exists <- file.exists(files_abs)
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332 files[exists] <- files_abs[exists]
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333 files[exists] <- sub("//","/",files[exists])
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334
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335 # WHAT IS ON THE FILESYSTEM
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336 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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337 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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338
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339 # COMPARISON
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340 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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341 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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342 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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343 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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344 }
2
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345 }
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346
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347
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348 #This function list the compatible files within the directory as xcms did
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349 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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350 getMSFiles <- function (directory) {
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351 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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352 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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353 info <- file.info(directory)
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354 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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355 files <- c(directory[!info$isdir], listed)
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356 exists <- file.exists(files)
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357 files <- files[exists]
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358 return(files)
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359 }
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360
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361 # This function check if XML contains special caracters. It also checks integrity and completness.
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362 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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363 checkXmlStructure <- function (directory) {
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364 cat("Checking XML structure...\n")
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365
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366 cmd <- paste0("IFS=$'\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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367 capture <- system(cmd, intern=TRUE)
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368
8
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369 if (length(capture)>0){
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370 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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371 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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372 write(capture, stderr())
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373 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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374 }
7
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375
2
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376 }
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377
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378
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379 # This function check if XML contain special characters
2
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380 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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381 deleteXmlBadCharacters<- function (directory) {
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382 cat("Checking Non ASCII characters in the XML...\n")
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383
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384 processed <- F
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385 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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386 for (i in l){
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387 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
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388 capture <- suppressWarnings(system(cmd, intern=TRUE))
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389 if (length(capture)>0){
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390 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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391 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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392 c <- system(cmd, intern=TRUE)
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393 capture <- ""
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394 processed <- T
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395 }
2
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396 }
8
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397 if (processed) cat("\n\n")
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398 return(processed)
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399 }
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400
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401
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402 # This function will compute MD5 checksum to check the data integrity
2
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403 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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404 getMd5sum <- function (directory) {
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405 cat("Compute md5 checksum...\n")
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406 # WHAT XCMS WILL FIND
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407 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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408 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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409 info <- file.info(directory)
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410 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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411 files <- c(directory[!info$isdir], listed)
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412 exists <- file.exists(files)
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413 files <- files[exists]
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414
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415 library(tools)
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416
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417 #cat("\n\n")
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418
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419 return(as.matrix(md5sum(files)))
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420 }
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421
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422
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423 # This function get the raw file path from the arguments
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424 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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425 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
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426 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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427
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428 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
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429
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430 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
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431 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
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432 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
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433 }
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434 if (exists("singlefile_galaxyPaths")){
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435 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
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436 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
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437
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438 singlefile <- NULL
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439 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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440 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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441 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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442 # In case, an url is used to import data within Galaxy
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443 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
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444 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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445 }
10
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446 }
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447 return(list(zipfile=zipfile, singlefile=singlefile))
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448 }
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449
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450 # This function retrieve the raw file in the working directory
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451 # - if zipfile: unzip the file with its directory tree
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452 # - if singlefiles: set symlink with the good filename
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453 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
8
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454 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
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455 if(!is.null(singlefile) && (length("singlefile")>0)) {
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456 for (singlefile_sampleName in names(singlefile)) {
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8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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457 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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458 if(!file.exists(singlefile_galaxyPath)){
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8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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459 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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lecorguille
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460 print(error_message); stop(error_message)
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 7
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461 }
2
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lecorguille
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462
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463 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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464 file.copy(singlefile_galaxyPath, singlefile_sampleName)
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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465
8
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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466 }
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lecorguille
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467 directory <- "."
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lecorguille
parents: 7
diff changeset
468
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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469 }
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8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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470 if(!is.null(zipfile) && (zipfile != "")) {
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4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
471 if(!file.exists(zipfile)){
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8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
472 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 7
diff changeset
473 print(error_message)
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 7
diff changeset
474 stop(error_message)
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 7
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475 }
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 7
diff changeset
476
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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477 #list all file in the zip file
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lecorguille
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478 #zip_files <- unzip(zipfile,list=T)[,"Name"]
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lecorguille
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479
8
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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480 #unzip
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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481 suppressWarnings(unzip(zipfile, unzip="unzip"))
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lecorguille
parents: 7
diff changeset
482
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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483 #get the directory name
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lecorguille
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484 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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485 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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486 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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487 directory <- "."
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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488 if (length(directories) == 1) directory <- directories
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lecorguille
parents: 7
diff changeset
489
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490 cat("files_root_directory\t",directory,"\n")
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lecorguille
parents: 7
diff changeset
491
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 7
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492 }
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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493 return (directory)
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494 }
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lecorguille
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495
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lecorguille
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496
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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497 # This function retrieve a xset like object
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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498 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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499 getxcmsSetObject <- function(xobject) {
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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500 # XCMS 1.x
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501 if (class(xobject) == "xcmsSet")
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lecorguille
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502 return (xobject)
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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503 # XCMS 3.x
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504 if (class(xobject) == "XCMSnExp") {
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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505 # Get the legacy xcmsSet object
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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506 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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lecorguille
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507 if (!is.null(xset@phenoData$sample_group))
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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508 sampclass(xset) <- xset@phenoData$sample_group
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lecorguille
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diff changeset
509 else
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
510 sampclass(xset) <- "."
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
511 return (xset)
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lecorguille
parents: 8
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512 }
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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513 }