Mercurial > repos > lecorguille > xcms_retcor

annotate lib.r @ 31:281786a7b9a2 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
author lecorguille
date Mon, 05 Mar 2018 04:17:36 -0500
parents 4d6f4cd7c3ef
children 69b5a006fca1
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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1 #@authors ABiMS TEAM, Y. Guitton
4d6f4cd7c3ef 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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lecorguille
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4 #@author G. Le Corguille
4d6f4cd7c3ef 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
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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6 parseCommandArgs <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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7 args <- batch::parseCommandArgs(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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8 for (key in names(args)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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9 if (args[key] %in% c("TRUE","FALSE"))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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10 args[key] = as.logical(args[key])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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11 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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12 return(args)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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13 }
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c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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15 #@author G. Le Corguille
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16 # This function will
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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17 # - load the packages
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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18 # - display the sessionInfo
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19 loadAndDisplayPackages <- function(pkgs) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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lecorguille
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22 sessioninfo = sessionInfo()
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23 cat(sessioninfo$R.version$version.string,"\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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24 cat("Main packages:\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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26 cat("Other loaded packages:\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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28 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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lecorguille
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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) {
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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33 if (convertRTMinute){
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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34 #converting the retention times (seconds) into minutes
c04568596f40 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
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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37 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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38 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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39 }
c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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40 return (variableMetadata)
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41 }
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42
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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$name),"_")
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47 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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48 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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49 variableMetadata <- cbind(name=variableMetadata$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$sample_group))]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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61 names(group_colors) <- unique(xdata$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 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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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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77 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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78 # Color by group
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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79 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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80 names(group_colors) <- unique(xdata$sample_group)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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81 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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82 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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83 # Color by sample
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84 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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85 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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86 dev.off()
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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87 }
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88
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89 #@author G. Le Corguille
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90 # value: intensity values to be used into, maxo or intb
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91 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
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92 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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93 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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94 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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95 variableMetadata <- featureDefinitions(xdata)
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96 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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97 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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98
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99 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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100 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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101
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102 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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103 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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104
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105 }
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106
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107 #@author Y. Guitton
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108 getBPC <- function(file,rtcor=NULL, ...) {
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109 object <- xcmsRaw(file)
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110 sel <- profRange(object, ...)
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111 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
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112 #plotChrom(xcmsRaw(file), base=T)
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113 }
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114
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115 #@author Y. Guitton
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116 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
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117 cat("Creating BIC pdf...\n")
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118
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119 if (is.null(xcmsSet)) {
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120 cat("Enter an xcmsSet \n")
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121 stop()
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122 } else {
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123 files <- filepaths(xcmsSet)
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124 }
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125
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126 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
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127
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128 classnames <- vector("list",length(phenoDataClass))
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129 for (i in 1:length(phenoDataClass)){
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130 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
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131 }
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132
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133 N <- dim(phenoData(xcmsSet))[1]
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134
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135 TIC <- vector("list",N)
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136
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137
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138 for (j in 1:N) {
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139
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140 TIC[[j]] <- getBPC(files[j])
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141 #good for raw
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142 # seems strange for corrected
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143 #errors if scanrange used in xcmsSetgeneration
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144 if (!is.null(xcmsSet) && rt == "corrected")
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145 rtcor <- xcmsSet@rt$corrected[[j]]
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146 else
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147 rtcor <- NULL
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148
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149 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
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150 # TIC[[j]][,1]<-rtcor
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151 }
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152
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153
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154
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155 pdf(pdfname,w=16,h=10)
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156 cols <- rainbow(N)
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157 lty <- 1:N
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158 pch <- 1:N
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159 #search for max x and max y in BPCs
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160 xlim <- range(sapply(TIC, function(x) range(x[,1])))
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161 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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162 ylim <- c(-ylim[2], ylim[2])
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163
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164
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165 ##plot start
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166
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167 if (length(phenoDataClass)>2){
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168 for (k in 1:(length(phenoDataClass)-1)){
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169 for (l in (k+1):length(phenoDataClass)){
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170 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
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171 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC")
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172 colvect <- NULL
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173 for (j in 1:length(classnames[[k]])) {
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174 tic <- TIC[[classnames[[k]][j]]]
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175 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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176 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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177 colvect <- append(colvect,cols[classnames[[k]][j]])
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178 }
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179 for (j in 1:length(classnames[[l]])) {
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180 # i <- class2names[j]
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181 tic <- TIC[[classnames[[l]][j]]]
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182 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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183 colvect <- append(colvect,cols[classnames[[l]][j]])
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184 }
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185 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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186 }
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187 }
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188 }#end if length >2
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189
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190 if (length(phenoDataClass)==2){
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191 k <- 1
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192 l <- 2
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193 colvect <- NULL
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194 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC")
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195
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196 for (j in 1:length(classnames[[k]])) {
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197
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198 tic <- TIC[[classnames[[k]][j]]]
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199 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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200 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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201 colvect<-append(colvect,cols[classnames[[k]][j]])
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202 }
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203 for (j in 1:length(classnames[[l]])) {
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204 # i <- class2names[j]
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205 tic <- TIC[[classnames[[l]][j]]]
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206 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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207 colvect <- append(colvect,cols[classnames[[l]][j]])
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208 }
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209 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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210
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211 }#end length ==2
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212
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213 #case where only one class
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214 if (length(phenoDataClass)==1){
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215 k <- 1
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216 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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217 colvect <- NULL
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218 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="BPC")
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219
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220 for (j in 1:length(classnames[[k]])) {
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221 tic <- TIC[[classnames[[k]][j]]]
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222 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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223 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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224 colvect <- append(colvect,cols[classnames[[k]][j]])
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225 }
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226
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227 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
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228
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229 }#end length ==1
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230
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231 dev.off() #pdf(pdfname,w=16,h=10)
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232
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233 invisible(TIC)
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234 }
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235
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236
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237
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238 #@author Y. Guitton
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239 getTIC <- function(file, rtcor=NULL) {
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240 object <- xcmsRaw(file)
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241 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object, mzrange=range(object@env$mz))$intensity)
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242 }
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243
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244 #overlay TIC from all files in current folder or from xcmsSet, create pdf
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245 #@author Y. Guitton
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246 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf", rt=c("raw","corrected")) {
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247 cat("Creating TIC pdf...\n")
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248
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249 if (is.null(xcmsSet)) {
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250 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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251 filepattern <- paste(paste("\\.", filepattern, "$", sep=""), collapse="|")
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252 if (is.null(files))
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253 files <- getwd()
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254 info <- file.info(files)
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255 listed <- list.files(files[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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256 files <- c(files[!info$isdir], listed)
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257 } else {
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258 files <- filepaths(xcmsSet)
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259 }
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260
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261 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
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262 classnames <- vector("list",length(phenoDataClass))
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263 for (i in 1:length(phenoDataClass)){
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264 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
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265 }
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266
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267 N <- length(files)
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268 TIC <- vector("list",N)
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269
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270 for (i in 1:N) {
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271 if (!is.null(xcmsSet) && rt == "corrected")
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272 rtcor <- xcmsSet@rt$corrected[[i]] else
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273 rtcor <- NULL
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274 TIC[[i]] <- getTIC(files[i], rtcor=rtcor)
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275 }
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276
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277 pdf(pdfname, w=16, h=10)
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278 cols <- rainbow(N)
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279 lty <- 1:N
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280 pch <- 1:N
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281 #search for max x and max y in TICs
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282 xlim <- range(sapply(TIC, function(x) range(x[,1])))
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283 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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284 ylim <- c(-ylim[2], ylim[2])
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285
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286
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287 ##plot start
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288 if (length(phenoDataClass)>2){
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289 for (k in 1:(length(phenoDataClass)-1)){
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290 for (l in (k+1):length(phenoDataClass)){
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291 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
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292 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC")
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293 colvect <- NULL
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294 for (j in 1:length(classnames[[k]])) {
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295 tic <- TIC[[classnames[[k]][j]]]
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296 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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297 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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298 colvect <- append(colvect,cols[classnames[[k]][j]])
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299 }
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300 for (j in 1:length(classnames[[l]])) {
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301 # i=class2names[j]
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302 tic <- TIC[[classnames[[l]][j]]]
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303 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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304 colvect <- append(colvect,cols[classnames[[l]][j]])
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305 }
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306 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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307 }
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308 }
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309 }#end if length >2
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310 if (length(phenoDataClass)==2){
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311 k <- 1
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312 l <- 2
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313
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314 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC")
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315 colvect <- NULL
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316 for (j in 1:length(classnames[[k]])) {
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317 tic <- TIC[[classnames[[k]][j]]]
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318 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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319 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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320 colvect <- append(colvect,cols[classnames[[k]][j]])
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321 }
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322 for (j in 1:length(classnames[[l]])) {
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323 # i <- class2names[j]
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324 tic <- TIC[[classnames[[l]][j]]]
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325 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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326 colvect <- append(colvect,cols[classnames[[l]][j]])
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327 }
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328 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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329
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330 }#end length ==2
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331
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332 #case where only one class
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333 if (length(phenoDataClass)==1){
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334 k <- 1
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335 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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336
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337 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="TIC")
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338 colvect <- NULL
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339 for (j in 1:length(classnames[[k]])) {
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340 tic <- TIC[[classnames[[k]][j]]]
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341 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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342 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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343 colvect <- append(colvect,cols[classnames[[k]][j]])
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344 }
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345
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346 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
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347
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348 }#end length ==1
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349
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350 dev.off() #pdf(pdfname,w=16,h=10)
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351
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352 invisible(TIC)
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353 }
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354
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355
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356
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357 # Get the polarities from all the samples of a condition
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358 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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359 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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360 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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361 cat("Creating the sampleMetadata file...\n")
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362
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363 #Create the sampleMetada dataframe
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364 sampleMetadata <- xdata@phenoData@data
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365 rownames(sampleMetadata) <- NULL
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366 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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367
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368 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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369 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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370
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371 if (any(duplicated(sampleNamesMakeNames))) {
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372 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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373 for (sampleName in sampleNamesOrigin) {
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374 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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375 }
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376 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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377 }
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378
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379 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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380 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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381 for (sampleName in sampleNamesOrigin) {
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382 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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383 }
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384 }
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385
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386 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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387
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388
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389 #For each sample file, the following actions are done
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390 for (fileIdx in 1:length(fileNames(xdata))) {
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391 #Check if the file is in the CDF format
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392 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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393
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394 # If the column isn't exist, with add one filled with NA
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395 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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396
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397 #Extract the polarity (a list of polarities)
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398 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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399 #Verify if all the scans have the same polarity
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400 uniq_list <- unique(polarity)
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401 if (length(uniq_list)>1){
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402 polarity <- "mixed"
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403 } else {
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404 polarity <- as.character(uniq_list)
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405 }
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406
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407 #Set the polarity attribute
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408 sampleMetadata$polarity[fileIdx] <- polarity
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409 }
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410
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411 }
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412
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413 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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414
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415 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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416
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417 }
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418
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419
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420 # This function check if xcms will found all the files
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421 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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422 checkFilesCompatibilityWithXcms <- function(directory) {
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423 cat("Checking files filenames compatibilities with xmcs...\n")
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424 # WHAT XCMS WILL FIND
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425 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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426 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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427 info <- file.info(directory)
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428 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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429 files <- c(directory[!info$isdir], listed)
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430 files_abs <- file.path(getwd(), files)
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431 exists <- file.exists(files_abs)
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432 files[exists] <- files_abs[exists]
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433 files[exists] <- sub("//","/",files[exists])
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434
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435 # WHAT IS ON THE FILESYSTEM
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436 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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437 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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438
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439 # COMPARISON
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440 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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441 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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442 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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443 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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444 }
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445 }
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446
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447
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448 #This function list the compatible files within the directory as xcms did
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449 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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450 getMSFiles <- function (directory) {
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451 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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452 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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453 info <- file.info(directory)
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454 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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455 files <- c(directory[!info$isdir], listed)
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456 exists <- file.exists(files)
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457 files <- files[exists]
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458 return(files)
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459 }
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460
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461 # This function check if XML contains special caracters. It also checks integrity and completness.
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462 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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463 checkXmlStructure <- function (directory) {
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464 cat("Checking XML structure...\n")
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465
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466 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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467 capture <- system(cmd, intern=TRUE)
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468
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469 if (length(capture)>0){
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470 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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471 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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472 write(capture, stderr())
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473 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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474 }
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475
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476 }
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477
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478
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479 # This function check if XML contain special characters
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480 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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481 deleteXmlBadCharacters<- function (directory) {
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482 cat("Checking Non ASCII characters in the XML...\n")
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483
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484 processed <- F
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485 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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486 for (i in l){
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487 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
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488 capture <- suppressWarnings(system(cmd, intern=TRUE))
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489 if (length(capture)>0){
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490 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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491 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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492 c <- system(cmd, intern=TRUE)
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493 capture <- ""
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494 processed <- T
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495 }
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496 }
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497 if (processed) cat("\n\n")
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498 return(processed)
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499 }
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500
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501
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502 # This function will compute MD5 checksum to check the data integrity
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503 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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504 getMd5sum <- function (directory) {
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505 cat("Compute md5 checksum...\n")
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506 # WHAT XCMS WILL FIND
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507 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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508 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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509 info <- file.info(directory)
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510 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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511 files <- c(directory[!info$isdir], listed)
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512 exists <- file.exists(files)
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513 files <- files[exists]
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514
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515 library(tools)
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516
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517 #cat("\n\n")
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518
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519 return(as.matrix(md5sum(files)))
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520 }
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521
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522
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523 # This function get the raw file path from the arguments
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524 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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525 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
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526 if (!is.null(args$zipfile)) zipfile <- args$zipfile
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527 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
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528 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
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529
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530 if (!is.null(args$singlefile_galaxyPath)) {
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531 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
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532 singlefile_sampleNames <- args$singlefile_sampleName
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533 }
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534 if (!is.null(args$singlefile_galaxyPathPositive)) {
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535 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
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536 singlefile_sampleNames <- args$singlefile_sampleNamePositive
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537 }
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538 if (!is.null(args$singlefile_galaxyPathNegative)) {
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539 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
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540 singlefile_sampleNames <- args$singlefile_sampleNameNegative
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541 }
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542 if (exists("singlefile_galaxyPaths")){
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543 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
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544 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
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545
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546 singlefile <- NULL
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547 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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548 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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549 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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550 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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551 }
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552 }
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553 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
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554 args[[argument]] <- NULL
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555 }
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556 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
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557 }
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558
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559
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560 # This function retrieve the raw file in the working directory
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561 # - if zipfile: unzip the file with its directory tree
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562 # - if singlefiles: set symlink with the good filename
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563 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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564 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
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565 if(!is.null(singlefile) && (length("singlefile")>0)) {
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566 for (singlefile_sampleName in names(singlefile)) {
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567 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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568 if(!file.exists(singlefile_galaxyPath)){
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569 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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570 print(error_message); stop(error_message)
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571 }
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572
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573 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
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574 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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575
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576 }
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577 directory <- "."
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578
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579 }
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580 if(!is.null(zipfile) && (zipfile != "")) {
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581 if(!file.exists(zipfile)){
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582 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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583 print(error_message)
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584 stop(error_message)
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585 }
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586
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587 #list all file in the zip file
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588 #zip_files <- unzip(zipfile,list=T)[,"Name"]
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589
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590 #unzip
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591 suppressWarnings(unzip(zipfile, unzip="unzip"))
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592
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593 #get the directory name
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594 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
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595 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
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596 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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597 directory <- "."
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598 if (length(directories) == 1) directory <- directories
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599
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600 cat("files_root_directory\t",directory,"\n")
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601
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602 }
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603 return (directory)
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604 }
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605
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606
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607 # This function retrieve a xset like object
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608 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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609 getxcmsSetObject <- function(xobject) {
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610 # XCMS 1.x
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611 if (class(xobject) == "xcmsSet")
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612 return (xobject)
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613 # XCMS 3.x
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614 if (class(xobject) == "XCMSnExp") {
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615 # Get the legacy xcmsSet object
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616 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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617 sampclass(xset) <- xset@phenoData$sample_group
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618 return (xset)
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619 }
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620 }
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621
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622
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623 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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624 # https://github.com/sneumann/xcms/issues/250
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625 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
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626 mzfmt <- paste("%.", mzdec, "f", sep = "")
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627 rtfmt <- paste("%.", rtdec, "f", sep = "")
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628
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629 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
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630 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
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631
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632 if (any(dup <- duplicated(gnames)))
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633 for (dupname in unique(gnames[dup])) {
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634 dupidx <- which(gnames == dupname)
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635 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
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636 }
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637
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638 return (gnames)
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639 }
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640
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641 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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642 # https://github.com/sneumann/xcms/issues/247
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643 .concatenate_XCMSnExp <- function(...) {
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644 x <- list(...)
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645 if (length(x) == 0)
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646 return(NULL)
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647 if (length(x) == 1)
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648 return(x[[1]])
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649 ## Check that all are XCMSnExp objects.
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650 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
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diff changeset
651 stop("All passed objects should be 'XCMSnExp' objects")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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652 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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653 ## If any of the XCMSnExp has alignment results or detected features drop
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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654 ## them!
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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655 x <- lapply(x, function(z) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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656 if (hasAdjustedRtime(z)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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657 z <- dropAdjustedRtime(z)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
658 warning("Adjusted retention times found, had to drop them.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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659 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
660 if (hasFeatures(z)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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661 z <- dropFeatureDefinitions(z)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
662 warning("Feature definitions found, had to drop them.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
663 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
664 z
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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665 })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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666 ## Combine peaks
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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667 fls <- lapply(x, fileNames)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
668 startidx <- cumsum(lengths(fls))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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669 pks <- lapply(x, chromPeaks)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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670 procH <- lapply(x, processHistory)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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671 for (i in 2:length(fls)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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672 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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673 procH[[i]] <- lapply(procH[[i]], function(z) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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674 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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675 z
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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676 })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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677 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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678 pks <- do.call(rbind, pks)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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679 new_x@.processHistory <- unlist(procH)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
680 chromPeaks(new_x) <- pks
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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681 if (validObject(new_x))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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682 new_x
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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683 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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684
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
685 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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686 # https://github.com/sneumann/xcms/issues/247
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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687 .concatenate_OnDiskMSnExp <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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688 x <- list(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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689 if (length(x) == 0)
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690 return(NULL)
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691 if (length(x) == 1)
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692 return(x[[1]])
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diff changeset
693 ## Check that all are XCMSnExp objects.
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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694 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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695 stop("All passed objects should be 'OnDiskMSnExp' objects")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
696 ## Check processingQueue
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diff changeset
697 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
698 new_procQ <- procQ[[1]]
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699 is_ok <- unlist(lapply(procQ, function(z)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
700 !is.character(all.equal(new_procQ, z))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
701 ))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
702 if (any(!is_ok)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
703 warning("Processing queues from the submitted objects differ! ",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
704 "Dropping the processing queue.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
705 new_procQ <- list()
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
706 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
707 ## processingData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
708 fls <- lapply(x, function(z) z@processingData@files)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
709 startidx <- cumsum(lengths(fls))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
710 ## featureData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
711 featd <- lapply(x, fData)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
712 ## Have to update the file index and the spectrum names.
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
713 for (i in 2:length(featd)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
714 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
715 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
716 fileIds = featd[[i]]$fileIdx,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
717 spectrumIds = featd[[i]]$spIdx,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
718 nSpectra = nrow(featd[[i]]),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
719 nFiles = length(unlist(fls))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
720 )
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
721 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
722 featd <- do.call(rbind, featd)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
723 featd$spectrum <- 1:nrow(featd)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
724 ## experimentData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
725 expdata <- lapply(x, function(z) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
726 ed <- z@experimentData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
727 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
728 instrumentModel = ed@instrumentModel,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
729 ionSource = ed@ionSource,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
730 analyser = ed@analyser,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
731 detectorType = ed@detectorType,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
732 stringsAsFactors = FALSE)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
733 })
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
734 expdata <- do.call(rbind, expdata)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
735 expdata <- new("MIAPE",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
736 instrumentManufacturer = expdata$instrumentManufacturer,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
737 instrumentModel = expdata$instrumentModel,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
738 ionSource = expdata$ionSource,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
739 analyser = expdata$analyser,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
740 detectorType = expdata$detectorType)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
741
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
742 ## protocolData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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743 protodata <- lapply(x, function(z) z@protocolData)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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744 if (any(unlist(lapply(protodata, nrow)) > 0))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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745 warning("Found non-empty protocol data, but merging protocol data is",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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746 " currently not supported. Skipped.")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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747 ## phenoData
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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748 pdata <- do.call(rbind, lapply(x, pData))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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749 res <- new(
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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750 "OnDiskMSnExp",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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751 phenoData = new("NAnnotatedDataFrame", data = pdata),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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752 featureData = new("AnnotatedDataFrame", featd),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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753 processingData = new("MSnProcess",
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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754 processing = paste0("Concatenated [", date(), "]"),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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755 files = unlist(fls), smoothed = NA),
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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756 experimentData = expdata,
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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757 spectraProcessingQueue = new_procQ)
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lecorguille
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758 if (validObject(res))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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759 res
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lecorguille
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760 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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761
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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762 #@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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763 # https://github.com/sneumann/xcms/issues/247
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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764 c.XCMSnExp <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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765 .concatenate_XCMSnExp(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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766 }