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annotate lib.r @ 32:565693681374 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
author lecorguille
date Mon, 05 Mar 2018 04:18:16 -0500
parents 8fd5b5afa24d
children ea611367e1da
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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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1 #@authors ABiMS TEAM, Y. Guitton
8fd5b5afa24d 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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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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4 #@author G. Le Corguille
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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6 parseCommandArgs <- function(...) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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7 args <- batch::parseCommandArgs(...)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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8 for (key in names(args)) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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9 if (args[key] %in% c("TRUE","FALSE"))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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10 args[key] = as.logical(args[key])
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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11 }
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lecorguille
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12 return(args)
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13 }
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1c78d61fd646 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
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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17 # - load the packages
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lecorguille
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18 # - display the sessionInfo
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19 loadAndDisplayPackages <- function(pkgs) {
8fd5b5afa24d 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)))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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lecorguille
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22 sessioninfo = sessionInfo()
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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23 cat(sessioninfo$R.version$version.string,"\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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24 cat("Main packages:\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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26 cat("Other loaded packages:\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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28 }
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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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30 #@author G. Le Corguille
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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31 # This function convert if it is required the Retention Time in minutes
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lecorguille
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32 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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33 if (convertRTMinute){
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 14
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34 #converting the retention times (seconds) into minutes
1c78d61fd646 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
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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37 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
8fd5b5afa24d 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 }
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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40 return (variableMetadata)
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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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$name),"_")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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47 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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48 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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49 variableMetadata <- cbind(name=variableMetadata$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))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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60 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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61 names(group_colors) <- unique(xdata$sample_group)
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63 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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64 for (i in 1:nrow(featureDefinitions(xdata))) {
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65 mzmin = featureDefinitions(xdata)[i,]$mzmin
565693681374 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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66 mzmax = featureDefinitions(xdata)[i,]$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)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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69 }
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71 dev.off()
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72 }
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74 #@author G. Le Corguille
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lecorguille
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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
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lecorguille
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79 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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80 names(group_colors) <- unique(xdata$sample_group)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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81 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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82 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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83 # Color by sample
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84 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
8fd5b5afa24d 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)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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86 dev.off()
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87 }
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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
31
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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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lecorguille
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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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diff changeset
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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lecorguille
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diff changeset
572
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573 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
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lecorguille
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574 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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diff changeset
575
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576 }
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577 directory <- "."
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diff changeset
578
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lecorguille
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579 }
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580 if(!is.null(zipfile) && (zipfile != "")) {
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lecorguille
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diff changeset
581 if(!file.exists(zipfile)){
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lecorguille
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diff changeset
582 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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lecorguille
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583 print(error_message)
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lecorguille
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diff changeset
584 stop(error_message)
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lecorguille
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585 }
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lecorguille
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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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diff changeset
589
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lecorguille
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590 #unzip
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lecorguille
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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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diff changeset
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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diff changeset
637
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638 return (gnames)
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lecorguille
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639 }
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diff changeset
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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diff changeset
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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651 stop("All passed objects should be 'XCMSnExp' objects")
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652 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
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653 ## If any of the XCMSnExp has alignment results or detected features drop
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diff changeset
654 ## them!
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
655 x <- lapply(x, function(z) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
656 if (hasAdjustedRtime(z)) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
657 z <- dropAdjustedRtime(z)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
658 warning("Adjusted retention times found, had to drop them.")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
659 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
660 if (hasFeatures(z)) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
661 z <- dropFeatureDefinitions(z)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
662 warning("Feature definitions found, had to drop them.")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
663 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
664 z
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
665 })
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
666 ## Combine peaks
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
667 fls <- lapply(x, fileNames)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
668 startidx <- cumsum(lengths(fls))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
669 pks <- lapply(x, chromPeaks)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
670 procH <- lapply(x, processHistory)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
671 for (i in 2:length(fls)) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
672 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
673 procH[[i]] <- lapply(procH[[i]], function(z) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
674 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
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lecorguille
parents: 30
diff changeset
675 z
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
676 })
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
677 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
678 pks <- do.call(rbind, pks)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
679 new_x@.processHistory <- unlist(procH)
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lecorguille
parents: 30
diff changeset
680 chromPeaks(new_x) <- pks
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
681 if (validObject(new_x))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
682 new_x
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
683 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
684
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
685 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
686 # https://github.com/sneumann/xcms/issues/247
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lecorguille
parents: 30
diff changeset
687 .concatenate_OnDiskMSnExp <- function(...) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
688 x <- list(...)
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lecorguille
parents: 30
diff changeset
689 if (length(x) == 0)
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lecorguille
parents: 30
diff changeset
690 return(NULL)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
691 if (length(x) == 1)
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lecorguille
parents: 30
diff changeset
692 return(x[[1]])
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lecorguille
parents: 30
diff changeset
693 ## Check that all are XCMSnExp objects.
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
694 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
695 stop("All passed objects should be 'OnDiskMSnExp' objects")
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lecorguille
parents: 30
diff changeset
696 ## Check processingQueue
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lecorguille
parents: 30
diff changeset
697 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
698 new_procQ <- procQ[[1]]
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lecorguille
parents: 30
diff changeset
699 is_ok <- unlist(lapply(procQ, function(z)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
700 !is.character(all.equal(new_procQ, z))
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lecorguille
parents: 30
diff changeset
701 ))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
702 if (any(!is_ok)) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
703 warning("Processing queues from the submitted objects differ! ",
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
704 "Dropping the processing queue.")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
705 new_procQ <- list()
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
706 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
707 ## processingData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
708 fls <- lapply(x, function(z) z@processingData@files)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
709 startidx <- cumsum(lengths(fls))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
710 ## featureData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
711 featd <- lapply(x, fData)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
712 ## Have to update the file index and the spectrum names.
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
713 for (i in 2:length(featd)) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
714 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
715 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
716 fileIds = featd[[i]]$fileIdx,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
717 spectrumIds = featd[[i]]$spIdx,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
718 nSpectra = nrow(featd[[i]]),
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
719 nFiles = length(unlist(fls))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
720 )
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
721 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
722 featd <- do.call(rbind, featd)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
723 featd$spectrum <- 1:nrow(featd)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
724 ## experimentData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
725 expdata <- lapply(x, function(z) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
726 ed <- z@experimentData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
727 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
728 instrumentModel = ed@instrumentModel,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
729 ionSource = ed@ionSource,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
730 analyser = ed@analyser,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
731 detectorType = ed@detectorType,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
732 stringsAsFactors = FALSE)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
733 })
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
734 expdata <- do.call(rbind, expdata)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
735 expdata <- new("MIAPE",
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
736 instrumentManufacturer = expdata$instrumentManufacturer,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
737 instrumentModel = expdata$instrumentModel,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
738 ionSource = expdata$ionSource,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
739 analyser = expdata$analyser,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
740 detectorType = expdata$detectorType)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
741
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
742 ## protocolData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
743 protodata <- lapply(x, function(z) z@protocolData)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
744 if (any(unlist(lapply(protodata, nrow)) > 0))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
745 warning("Found non-empty protocol data, but merging protocol data is",
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
746 " currently not supported. Skipped.")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
747 ## phenoData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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748 pdata <- do.call(rbind, lapply(x, pData))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
749 res <- new(
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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750 "OnDiskMSnExp",
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
751 phenoData = new("NAnnotatedDataFrame", data = pdata),
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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752 featureData = new("AnnotatedDataFrame", featd),
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
753 processingData = new("MSnProcess",
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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754 processing = paste0("Concatenated [", date(), "]"),
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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755 files = unlist(fls), smoothed = NA),
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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756 experimentData = expdata,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
757 spectraProcessingQueue = new_procQ)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
758 if (validObject(res))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
759 res
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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760 }
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lecorguille
parents: 30
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761
8fd5b5afa24d 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
parents: 30
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763 # https://github.com/sneumann/xcms/issues/247
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lecorguille
parents: 30
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764 c.XCMSnExp <- function(...) {
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lecorguille
parents: 30
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765 .concatenate_XCMSnExp(...)
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lecorguille
parents: 30
diff changeset
766 }