Mercurial > repos > lecorguille > xcms_xcmsset

annotate lib.r @ 34:efd23113d5f4 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
author lecorguille
date Thu, 08 Mar 2018 05:51:32 -0500
parents c363b9f1caef
children 7f636ad1162b
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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1 #@authors ABiMS TEAM, Y. Guitton
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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4 #@author G. Le Corguille
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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6 parseCommandArgs <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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7 args <- batch::parseCommandArgs(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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8 for (key in names(args)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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9 if (args[key] %in% c("TRUE","FALSE"))
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lecorguille
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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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lecorguille
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15 #@author G. Le Corguille
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16 # This function will
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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)))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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26 cat("Other loaded packages:\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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28 }
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30 #@author G. Le Corguille
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lecorguille
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31 # This function convert if it is required the Retention Time in minutes
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32 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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33 if (convertRTMinute){
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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34 #converting the retention times (seconds) into minutes
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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35 print("converting the retention times into minutes in the variableMetadata")
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36 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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37 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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38 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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39 }
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40 return (variableMetadata)
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41 }
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43 #@author G. Le Corguille
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44 # This function format ions identifiers
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45 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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46 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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47 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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48 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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49 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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50 return(variableMetadata)
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51 }
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53 #@author G. Le Corguille
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54 # Draw the plotChromPeakDensity 3 per page in a pdf file
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55 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
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56 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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58 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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60 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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61 names(group_colors) <- unique(xdata$sample_group)
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63 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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64 for (i in 1:nrow(featureDefinitions(xdata))) {
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65 mzmin = featureDefinitions(xdata)[i,]$mzmin
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66 mzmax = featureDefinitions(xdata)[i,]$mzmax
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67 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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68 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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69 }
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71 dev.off()
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72 }
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74 #@author G. Le Corguille
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75 # Draw the plotChromPeakDensity 3 per page in a pdf file
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76 getPlotAdjustedRtime <- function(xdata) {
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78 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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80 # Color by group
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81 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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82 names(group_colors) <- unique(xdata$sample_group)
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83 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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84 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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86 # Color by sample
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87 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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88 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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89
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90 dev.off()
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91 }
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92
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93 #@author G. Le Corguille
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94 # value: intensity values to be used into, maxo or intb
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95 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
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96 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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97 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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98 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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99 variableMetadata <- featureDefinitions(xdata)
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100 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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101 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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102
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103 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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104 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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105
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106 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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107 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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108
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109 }
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110
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111 #@author G. Le Corguille
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112 getPlotChromatogram <- function(xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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113
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114 chrom <- chromatogram(xdata, aggregationFun = aggregationFun)
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115 if (aggregationFun == "sum")
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116 type="Total Ion Chromatograms"
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117 else
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118 type="Base Peak Intensity Chromatograms"
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119
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120 adjusted="Raw"
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121 if (hasAdjustedRtime(xdata))
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122 adjusted="Adjusted"
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123
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124 main <- paste(type,":",adjusted,"data")
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125
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126 pdf(pdfname, width=16, height=10)
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127
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128 # Color by group
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129 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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130 names(group_colors) <- unique(xdata$sample_group)
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131 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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132 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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133
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134 # Color by sample
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135 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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136 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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137
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138 dev.off()
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139 }
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140
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141 #@author G. Le Corguille
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142 getPlotTICs <- function(xdata, pdfname="TICs.pdf") {
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143 getPlotChromatogram(xdata, pdfname, aggregationFun = "sum")
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144 }
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145
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146 #@author G. Le Corguille
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147 getPlotBPIs <- function(xdata, pdfname="BPIs.pdf") {
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148 getPlotChromatogram(xdata, pdfname, aggregationFun = "max")
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149 }
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150
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151
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152 # Get the polarities from all the samples of a condition
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153 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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154 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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155 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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156 cat("Creating the sampleMetadata file...\n")
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157
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158 #Create the sampleMetada dataframe
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159 sampleMetadata <- xdata@phenoData@data
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160 rownames(sampleMetadata) <- NULL
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161 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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162
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163 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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164 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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165
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166 if (any(duplicated(sampleNamesMakeNames))) {
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167 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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168 for (sampleName in sampleNamesOrigin) {
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169 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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170 }
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171 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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172 }
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173
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174 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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175 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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176 for (sampleName in sampleNamesOrigin) {
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177 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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178 }
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179 }
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180
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181 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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182
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183
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184 #For each sample file, the following actions are done
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185 for (fileIdx in 1:length(fileNames(xdata))) {
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186 #Check if the file is in the CDF format
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187 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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188
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189 # If the column isn't exist, with add one filled with NA
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190 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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191
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192 #Extract the polarity (a list of polarities)
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193 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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194 #Verify if all the scans have the same polarity
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195 uniq_list <- unique(polarity)
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196 if (length(uniq_list)>1){
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197 polarity <- "mixed"
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198 } else {
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199 polarity <- as.character(uniq_list)
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200 }
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201
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202 #Set the polarity attribute
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203 sampleMetadata$polarity[fileIdx] <- polarity
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204 }
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205
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206 }
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207
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208 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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209
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210 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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211
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212 }
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213
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214
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215 # This function check if xcms will found all the files
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216 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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217 checkFilesCompatibilityWithXcms <- function(directory) {
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218 cat("Checking files filenames compatibilities with xmcs...\n")
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219 # WHAT XCMS WILL FIND
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220 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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221 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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222 info <- file.info(directory)
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223 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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224 files <- c(directory[!info$isdir], listed)
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225 files_abs <- file.path(getwd(), files)
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226 exists <- file.exists(files_abs)
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227 files[exists] <- files_abs[exists]
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228 files[exists] <- sub("//","/",files[exists])
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229
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230 # WHAT IS ON THE FILESYSTEM
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231 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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232 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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233
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234 # COMPARISON
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235 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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236 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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237 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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238 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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239 }
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240 }
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241
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242
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243 #This function list the compatible files within the directory as xcms did
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244 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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245 getMSFiles <- function (directory) {
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246 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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247 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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248 info <- file.info(directory)
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249 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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250 files <- c(directory[!info$isdir], listed)
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251 exists <- file.exists(files)
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252 files <- files[exists]
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253 return(files)
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254 }
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255
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256 # This function check if XML contains special caracters. It also checks integrity and completness.
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257 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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258 checkXmlStructure <- function (directory) {
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259 cat("Checking XML structure...\n")
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260
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261 cmd <- paste0("IFS=$'\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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262 capture <- system(cmd, intern=TRUE)
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263
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264 if (length(capture)>0){
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265 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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266 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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267 write(capture, stderr())
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268 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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269 }
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270
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271 }
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272
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273
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274 # This function check if XML contain special characters
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275 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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276 deleteXmlBadCharacters<- function (directory) {
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277 cat("Checking Non ASCII characters in the XML...\n")
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278
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279 processed <- F
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280 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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281 for (i in l){
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282 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
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283 capture <- suppressWarnings(system(cmd, intern=TRUE))
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284 if (length(capture)>0){
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285 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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286 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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287 c <- system(cmd, intern=TRUE)
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288 capture <- ""
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289 processed <- T
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290 }
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291 }
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292 if (processed) cat("\n\n")
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293 return(processed)
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294 }
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295
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296
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297 # This function will compute MD5 checksum to check the data integrity
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298 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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299 getMd5sum <- function (directory) {
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300 cat("Compute md5 checksum...\n")
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301 # WHAT XCMS WILL FIND
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302 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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303 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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304 info <- file.info(directory)
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305 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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306 files <- c(directory[!info$isdir], listed)
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307 exists <- file.exists(files)
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308 files <- files[exists]
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309
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310 library(tools)
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311
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312 #cat("\n\n")
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313
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314 return(as.matrix(md5sum(files)))
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315 }
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316
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317
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318 # This function get the raw file path from the arguments
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319 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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320 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
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321 if (!is.null(args$zipfile)) zipfile <- args$zipfile
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322 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
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323 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
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324
32
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325 if (!is.null(args$singlefile_galaxyPath)) {
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326 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
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327 singlefile_sampleNames <- args$singlefile_sampleName
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328 }
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329 if (!is.null(args$singlefile_galaxyPathPositive)) {
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330 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
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331 singlefile_sampleNames <- args$singlefile_sampleNamePositive
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332 }
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333 if (!is.null(args$singlefile_galaxyPathNegative)) {
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334 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
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335 singlefile_sampleNames <- args$singlefile_sampleNameNegative
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336 }
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337 if (exists("singlefile_galaxyPaths")){
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338 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
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339 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
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340
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341 singlefile <- NULL
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342 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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343 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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344 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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345 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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346 }
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347 }
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348 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
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349 args[[argument]] <- NULL
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350 }
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351 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
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352 }
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353
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354
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355 # This function retrieve the raw file in the working directory
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356 # - if zipfile: unzip the file with its directory tree
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357 # - if singlefiles: set symlink with the good filename
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358 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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359 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
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360 if(!is.null(singlefile) && (length("singlefile")>0)) {
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361 for (singlefile_sampleName in names(singlefile)) {
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362 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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363 if(!file.exists(singlefile_galaxyPath)){
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364 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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365 print(error_message); stop(error_message)
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366 }
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367
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368 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
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369 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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370
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371 }
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372 directory <- "."
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373
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374 }
32
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375 if(!is.null(zipfile) && (zipfile != "")) {
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376 if(!file.exists(zipfile)){
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377 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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378 print(error_message)
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379 stop(error_message)
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380 }
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381
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382 #list all file in the zip file
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383 #zip_files <- unzip(zipfile,list=T)[,"Name"]
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384
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385 #unzip
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386 suppressWarnings(unzip(zipfile, unzip="unzip"))
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387
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388 #get the directory name
32
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389 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
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390 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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391 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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392 directory <- "."
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393 if (length(directories) == 1) directory <- directories
24
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394
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395 cat("files_root_directory\t",directory,"\n")
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396
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397 }
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398 return (directory)
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399 }
32
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400
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lecorguille
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401
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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402 # This function retrieve a xset like object
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403 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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404 getxcmsSetObject <- function(xobject) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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405 # XCMS 1.x
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406 if (class(xobject) == "xcmsSet")
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407 return (xobject)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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408 # XCMS 3.x
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409 if (class(xobject) == "XCMSnExp") {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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410 # Get the legacy xcmsSet object
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411 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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412 sampclass(xset) <- xset@phenoData$sample_group
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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413 return (xset)
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lecorguille
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414 }
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lecorguille
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415 }
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416
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417
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418 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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419 # https://github.com/sneumann/xcms/issues/250
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420 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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421 mzfmt <- paste("%.", mzdec, "f", sep = "")
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422 rtfmt <- paste("%.", rtdec, "f", sep = "")
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diff changeset
423
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424 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
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425 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
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426
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427 if (any(dup <- duplicated(gnames)))
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428 for (dupname in unique(gnames[dup])) {
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429 dupidx <- which(gnames == dupname)
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430 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
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431 }
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432
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433 return (gnames)
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lecorguille
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434 }
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435
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436 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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lecorguille
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437 # https://github.com/sneumann/xcms/issues/247
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438 .concatenate_XCMSnExp <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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439 x <- list(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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440 if (length(x) == 0)
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441 return(NULL)
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442 if (length(x) == 1)
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diff changeset
443 return(x[[1]])
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444 ## Check that all are XCMSnExp objects.
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445 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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446 stop("All passed objects should be 'XCMSnExp' objects")
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447 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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448 ## If any of the XCMSnExp has alignment results or detected features drop
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449 ## them!
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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450 x <- lapply(x, function(z) {
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lecorguille
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451 if (hasAdjustedRtime(z)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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452 z <- dropAdjustedRtime(z)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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453 warning("Adjusted retention times found, had to drop them.")
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454 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
455 if (hasFeatures(z)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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456 z <- dropFeatureDefinitions(z)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
457 warning("Feature definitions found, had to drop them.")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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458 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
459 z
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
460 })
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
461 ## Combine peaks
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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462 fls <- lapply(x, fileNames)
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lecorguille
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diff changeset
463 startidx <- cumsum(lengths(fls))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
464 pks <- lapply(x, chromPeaks)
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diff changeset
465 procH <- lapply(x, processHistory)
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diff changeset
466 for (i in 2:length(fls)) {
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467 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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468 procH[[i]] <- lapply(procH[[i]], function(z) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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469 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
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diff changeset
470 z
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471 })
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472 }
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473 pks <- do.call(rbind, pks)
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474 new_x@.processHistory <- unlist(procH)
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475 chromPeaks(new_x) <- pks
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476 if (validObject(new_x))
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477 new_x
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478 }
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479
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480 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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481 # https://github.com/sneumann/xcms/issues/247
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482 .concatenate_OnDiskMSnExp <- function(...) {
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483 x <- list(...)
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484 if (length(x) == 0)
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485 return(NULL)
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486 if (length(x) == 1)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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487 return(x[[1]])
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488 ## Check that all are XCMSnExp objects.
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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489 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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490 stop("All passed objects should be 'OnDiskMSnExp' objects")
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491 ## Check processingQueue
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492 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
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493 new_procQ <- procQ[[1]]
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494 is_ok <- unlist(lapply(procQ, function(z)
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495 !is.character(all.equal(new_procQ, z))
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496 ))
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497 if (any(!is_ok)) {
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498 warning("Processing queues from the submitted objects differ! ",
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499 "Dropping the processing queue.")
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500 new_procQ <- list()
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501 }
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502 ## processingData
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503 fls <- lapply(x, function(z) z@processingData@files)
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504 startidx <- cumsum(lengths(fls))
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505 ## featureData
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506 featd <- lapply(x, fData)
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507 ## Have to update the file index and the spectrum names.
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508 for (i in 2:length(featd)) {
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509 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
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510 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
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511 fileIds = featd[[i]]$fileIdx,
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512 spectrumIds = featd[[i]]$spIdx,
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513 nSpectra = nrow(featd[[i]]),
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514 nFiles = length(unlist(fls))
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lecorguille
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515 )
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516 }
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517 featd <- do.call(rbind, featd)
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518 featd$spectrum <- 1:nrow(featd)
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519 ## experimentData
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520 expdata <- lapply(x, function(z) {
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521 ed <- z@experimentData
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522 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
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diff changeset
523 instrumentModel = ed@instrumentModel,
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diff changeset
524 ionSource = ed@ionSource,
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diff changeset
525 analyser = ed@analyser,
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diff changeset
526 detectorType = ed@detectorType,
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527 stringsAsFactors = FALSE)
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diff changeset
528 })
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diff changeset
529 expdata <- do.call(rbind, expdata)
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diff changeset
530 expdata <- new("MIAPE",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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531 instrumentManufacturer = expdata$instrumentManufacturer,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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532 instrumentModel = expdata$instrumentModel,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
533 ionSource = expdata$ionSource,
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diff changeset
534 analyser = expdata$analyser,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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535 detectorType = expdata$detectorType)
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diff changeset
536
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
537 ## protocolData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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538 protodata <- lapply(x, function(z) z@protocolData)
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539 if (any(unlist(lapply(protodata, nrow)) > 0))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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540 warning("Found non-empty protocol data, but merging protocol data is",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
541 " currently not supported. Skipped.")
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lecorguille
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diff changeset
542 ## phenoData
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543 pdata <- do.call(rbind, lapply(x, pData))
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diff changeset
544 res <- new(
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diff changeset
545 "OnDiskMSnExp",
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546 phenoData = new("NAnnotatedDataFrame", data = pdata),
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diff changeset
547 featureData = new("AnnotatedDataFrame", featd),
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lecorguille
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diff changeset
548 processingData = new("MSnProcess",
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549 processing = paste0("Concatenated [", date(), "]"),
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diff changeset
550 files = unlist(fls), smoothed = NA),
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551 experimentData = expdata,
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lecorguille
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diff changeset
552 spectraProcessingQueue = new_procQ)
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diff changeset
553 if (validObject(res))
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diff changeset
554 res
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diff changeset
555 }
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lecorguille
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diff changeset
556
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
557 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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lecorguille
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558 # https://github.com/sneumann/xcms/issues/247
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diff changeset
559 c.XCMSnExp <- function(...) {
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diff changeset
560 .concatenate_XCMSnExp(...)
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561 }