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annotate lib.r @ 31:8fd5b5afa24d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
author lecorguille
date Thu, 01 Mar 2018 04:17:29 -0500
parents 6b5ed508f81f
children 565693681374
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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
parents: 30
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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
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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])
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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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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
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17 # - load the packages
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18 # - display the sessionInfo
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19 loadAndDisplayPackages <- function(pkgs) {
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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22 sessioninfo = sessionInfo()
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23 cat(sessioninfo$R.version$version.string,"\n")
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24 cat("Main packages:\n")
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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26 cat("Other loaded packages:\n")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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27 for (pkg in names(sessioninfo$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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30 #@author G. Le Corguille
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lecorguille
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31 # This function convert if it is required the Retention Time in minutes
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32 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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33 if (convertRTMinute){
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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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
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37 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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38 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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39 }
1c78d61fd646 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$name),"_")
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47 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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48 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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49 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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50 return(variableMetadata)
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51 }
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53 #@author G. Le Corguille
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54 # Draw the plotChromPeakDensity 3 per page in a pdf file
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55 getPlotChromPeakDensity <- function(xdata) {
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56 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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58 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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60 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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61 names(group_colors) <- unique(xdata$sample_group)
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63 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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64 for (i in 1:nrow(featureDefinitions(xdata))) {
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65 plotChromPeakDensity(xdata, mz=c(featureDefinitions(xdata)[i,]$mzmin,featureDefinitions(xdata)[i,]$mzmax), col=group_colors, pch=16, xlim=xlim)
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66 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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67 }
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69 dev.off()
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70 }
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72 #@author G. Le Corguille
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73 # Draw the plotChromPeakDensity 3 per page in a pdf file
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74 getPlotAdjustedRtime <- function(xdata) {
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75 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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76 # Color by group
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77 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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78 names(group_colors) <- unique(xdata$sample_group)
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79 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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80 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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81 # Color by sample
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82 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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83 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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84 dev.off()
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85 }
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87 #@author G. Le Corguille
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88 # value: intensity values to be used into, maxo or intb
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89 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
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90 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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91 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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92 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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93 variableMetadata <- featureDefinitions(xdata)
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94 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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95 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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96
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97 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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98 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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99
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100 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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101 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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102
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103 }
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104
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105 #@author Y. Guitton
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106 getBPC <- function(file,rtcor=NULL, ...) {
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107 object <- xcmsRaw(file)
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108 sel <- profRange(object, ...)
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109 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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110 #plotChrom(xcmsRaw(file), base=T)
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111 }
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112
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113 #@author Y. Guitton
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114 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
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115 cat("Creating BIC pdf...\n")
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116
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117 if (is.null(xcmsSet)) {
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118 cat("Enter an xcmsSet \n")
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119 stop()
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120 } else {
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121 files <- filepaths(xcmsSet)
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122 }
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123
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124 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
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125
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126 classnames <- vector("list",length(phenoDataClass))
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127 for (i in 1:length(phenoDataClass)){
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128 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
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129 }
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130
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131 N <- dim(phenoData(xcmsSet))[1]
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132
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133 TIC <- vector("list",N)
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134
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135
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136 for (j in 1:N) {
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137
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138 TIC[[j]] <- getBPC(files[j])
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139 #good for raw
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140 # seems strange for corrected
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141 #errors if scanrange used in xcmsSetgeneration
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142 if (!is.null(xcmsSet) && rt == "corrected")
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143 rtcor <- xcmsSet@rt$corrected[[j]]
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144 else
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145 rtcor <- NULL
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146
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147 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
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148 # TIC[[j]][,1]<-rtcor
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149 }
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150
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151
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152
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153 pdf(pdfname,w=16,h=10)
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154 cols <- rainbow(N)
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155 lty <- 1:N
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156 pch <- 1:N
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157 #search for max x and max y in BPCs
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158 xlim <- range(sapply(TIC, function(x) range(x[,1])))
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159 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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160 ylim <- c(-ylim[2], ylim[2])
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161
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162
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163 ##plot start
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164
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165 if (length(phenoDataClass)>2){
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166 for (k in 1:(length(phenoDataClass)-1)){
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167 for (l in (k+1):length(phenoDataClass)){
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168 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
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169 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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170 colvect <- NULL
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171 for (j in 1:length(classnames[[k]])) {
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172 tic <- TIC[[classnames[[k]][j]]]
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173 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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174 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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175 colvect <- append(colvect,cols[classnames[[k]][j]])
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176 }
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177 for (j in 1:length(classnames[[l]])) {
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178 # i <- class2names[j]
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179 tic <- TIC[[classnames[[l]][j]]]
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180 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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181 colvect <- append(colvect,cols[classnames[[l]][j]])
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182 }
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183 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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184 }
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185 }
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186 }#end if length >2
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187
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188 if (length(phenoDataClass)==2){
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189 k <- 1
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190 l <- 2
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191 colvect <- NULL
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192 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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193
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194 for (j in 1:length(classnames[[k]])) {
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195
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196 tic <- TIC[[classnames[[k]][j]]]
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197 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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198 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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199 colvect<-append(colvect,cols[classnames[[k]][j]])
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200 }
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201 for (j in 1:length(classnames[[l]])) {
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202 # i <- class2names[j]
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203 tic <- TIC[[classnames[[l]][j]]]
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204 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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205 colvect <- append(colvect,cols[classnames[[l]][j]])
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206 }
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207 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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208
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209 }#end length ==2
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210
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211 #case where only one class
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212 if (length(phenoDataClass)==1){
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213 k <- 1
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214 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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215 colvect <- NULL
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216 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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217
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218 for (j in 1:length(classnames[[k]])) {
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219 tic <- TIC[[classnames[[k]][j]]]
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220 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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221 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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222 colvect <- append(colvect,cols[classnames[[k]][j]])
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223 }
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224
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225 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
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226
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227 }#end length ==1
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228
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229 dev.off() #pdf(pdfname,w=16,h=10)
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230
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231 invisible(TIC)
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232 }
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233
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234
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235
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236 #@author Y. Guitton
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237 getTIC <- function(file, rtcor=NULL) {
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238 object <- xcmsRaw(file)
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239 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object, mzrange=range(object@env$mz))$intensity)
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240 }
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241
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242 #overlay TIC from all files in current folder or from xcmsSet, create pdf
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243 #@author Y. Guitton
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244 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf", rt=c("raw","corrected")) {
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245 cat("Creating TIC pdf...\n")
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246
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247 if (is.null(xcmsSet)) {
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248 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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249 filepattern <- paste(paste("\\.", filepattern, "$", sep=""), collapse="|")
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250 if (is.null(files))
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251 files <- getwd()
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252 info <- file.info(files)
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253 listed <- list.files(files[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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254 files <- c(files[!info$isdir], listed)
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255 } else {
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256 files <- filepaths(xcmsSet)
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257 }
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258
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259 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
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260 classnames <- vector("list",length(phenoDataClass))
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261 for (i in 1:length(phenoDataClass)){
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262 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
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263 }
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264
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265 N <- length(files)
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266 TIC <- vector("list",N)
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267
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268 for (i in 1:N) {
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269 if (!is.null(xcmsSet) && rt == "corrected")
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270 rtcor <- xcmsSet@rt$corrected[[i]] else
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271 rtcor <- NULL
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272 TIC[[i]] <- getTIC(files[i], rtcor=rtcor)
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273 }
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274
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275 pdf(pdfname, w=16, h=10)
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276 cols <- rainbow(N)
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277 lty <- 1:N
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278 pch <- 1:N
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279 #search for max x and max y in TICs
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280 xlim <- range(sapply(TIC, function(x) range(x[,1])))
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281 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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282 ylim <- c(-ylim[2], ylim[2])
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283
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284
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285 ##plot start
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286 if (length(phenoDataClass)>2){
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287 for (k in 1:(length(phenoDataClass)-1)){
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288 for (l in (k+1):length(phenoDataClass)){
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289 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
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290 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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291 colvect <- NULL
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292 for (j in 1:length(classnames[[k]])) {
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293 tic <- TIC[[classnames[[k]][j]]]
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294 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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295 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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296 colvect <- append(colvect,cols[classnames[[k]][j]])
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297 }
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298 for (j in 1:length(classnames[[l]])) {
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299 # i=class2names[j]
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300 tic <- TIC[[classnames[[l]][j]]]
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301 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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302 colvect <- append(colvect,cols[classnames[[l]][j]])
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303 }
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304 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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305 }
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306 }
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307 }#end if length >2
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308 if (length(phenoDataClass)==2){
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309 k <- 1
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310 l <- 2
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311
31
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312 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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313 colvect <- NULL
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314 for (j in 1:length(classnames[[k]])) {
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315 tic <- TIC[[classnames[[k]][j]]]
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316 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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317 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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318 colvect <- append(colvect,cols[classnames[[k]][j]])
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319 }
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320 for (j in 1:length(classnames[[l]])) {
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321 # i <- class2names[j]
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322 tic <- TIC[[classnames[[l]][j]]]
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323 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
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324 colvect <- append(colvect,cols[classnames[[l]][j]])
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325 }
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326 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
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327
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328 }#end length ==2
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329
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330 #case where only one class
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331 if (length(phenoDataClass)==1){
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332 k <- 1
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333 ylim <- range(sapply(TIC, function(x) range(x[,2])))
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334
31
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335 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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336 colvect <- NULL
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337 for (j in 1:length(classnames[[k]])) {
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338 tic <- TIC[[classnames[[k]][j]]]
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339 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
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340 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
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341 colvect <- append(colvect,cols[classnames[[k]][j]])
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342 }
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343
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344 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
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345
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346 }#end length ==1
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347
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348 dev.off() #pdf(pdfname,w=16,h=10)
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349
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350 invisible(TIC)
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351 }
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352
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353
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354
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355 # Get the polarities from all the samples of a condition
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356 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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357 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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358 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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359 cat("Creating the sampleMetadata file...\n")
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360
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361 #Create the sampleMetada dataframe
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362 sampleMetadata <- xdata@phenoData@data
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363 rownames(sampleMetadata) <- NULL
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364 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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365
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366 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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367 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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368
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369 if (any(duplicated(sampleNamesMakeNames))) {
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370 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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371 for (sampleName in sampleNamesOrigin) {
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372 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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373 }
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374 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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375 }
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376
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377 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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378 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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379 for (sampleName in sampleNamesOrigin) {
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380 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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381 }
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382 }
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383
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384 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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385
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386
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387 #For each sample file, the following actions are done
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388 for (fileIdx in 1:length(fileNames(xdata))) {
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389 #Check if the file is in the CDF format
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390 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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391
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392 # If the column isn't exist, with add one filled with NA
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393 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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394
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395 #Extract the polarity (a list of polarities)
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396 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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397 #Verify if all the scans have the same polarity
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398 uniq_list <- unique(polarity)
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399 if (length(uniq_list)>1){
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400 polarity <- "mixed"
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401 } else {
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402 polarity <- as.character(uniq_list)
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403 }
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404
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405 #Set the polarity attribute
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406 sampleMetadata$polarity[fileIdx] <- polarity
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407 }
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408
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409 }
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410
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411 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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412
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413 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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414
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415 }
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416
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417
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418 # This function check if xcms will found all the files
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419 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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420 checkFilesCompatibilityWithXcms <- function(directory) {
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421 cat("Checking files filenames compatibilities with xmcs...\n")
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422 # WHAT XCMS WILL FIND
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423 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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424 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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425 info <- file.info(directory)
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426 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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427 files <- c(directory[!info$isdir], listed)
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428 files_abs <- file.path(getwd(), files)
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429 exists <- file.exists(files_abs)
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430 files[exists] <- files_abs[exists]
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431 files[exists] <- sub("//","/",files[exists])
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432
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433 # WHAT IS ON THE FILESYSTEM
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434 filesystem_filepaths <- system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
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435 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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436
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437 # COMPARISON
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438 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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439 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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440 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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441 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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442 }
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443 }
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444
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445
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446 #This function list the compatible files within the directory as xcms did
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447 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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448 getMSFiles <- function (directory) {
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449 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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450 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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451 info <- file.info(directory)
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452 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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453 files <- c(directory[!info$isdir], listed)
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454 exists <- file.exists(files)
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455 files <- files[exists]
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456 return(files)
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457 }
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458
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459 # This function check if XML contains special caracters. It also checks integrity and completness.
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460 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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461 checkXmlStructure <- function (directory) {
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462 cat("Checking XML structure...\n")
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463
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464 cmd <- paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
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465 capture <- system(cmd, intern=TRUE)
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466
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467 if (length(capture)>0){
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468 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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469 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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470 write(capture, stderr())
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471 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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472 }
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473
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474 }
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475
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476
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477 # This function check if XML contain special characters
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478 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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479 deleteXmlBadCharacters<- function (directory) {
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480 cat("Checking Non ASCII characters in the XML...\n")
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481
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482 processed <- F
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483 l <- system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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484 for (i in l){
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485 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
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486 capture <- suppressWarnings(system(cmd, intern=TRUE))
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487 if (length(capture)>0){
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488 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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489 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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490 c <- system(cmd, intern=TRUE)
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491 capture <- ""
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492 processed <- T
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493 }
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494 }
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495 if (processed) cat("\n\n")
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496 return(processed)
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497 }
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498
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499
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500 # This function will compute MD5 checksum to check the data integrity
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501 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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502 getMd5sum <- function (directory) {
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503 cat("Compute md5 checksum...\n")
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504 # WHAT XCMS WILL FIND
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505 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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506 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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507 info <- file.info(directory)
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508 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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509 files <- c(directory[!info$isdir], listed)
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510 exists <- file.exists(files)
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511 files <- files[exists]
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512
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513 library(tools)
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514
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515 #cat("\n\n")
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516
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517 return(as.matrix(md5sum(files)))
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518 }
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519
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520
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521 # This function get the raw file path from the arguments
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522 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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523 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
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524 if (!is.null(args$zipfile)) zipfile <- args$zipfile
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525 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
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526 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
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527
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528 if (!is.null(args$singlefile_galaxyPath)) {
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529 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
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530 singlefile_sampleNames <- args$singlefile_sampleName
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531 }
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532 if (!is.null(args$singlefile_galaxyPathPositive)) {
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533 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
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534 singlefile_sampleNames <- args$singlefile_sampleNamePositive
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535 }
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536 if (!is.null(args$singlefile_galaxyPathNegative)) {
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537 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
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538 singlefile_sampleNames <- args$singlefile_sampleNameNegative
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539 }
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540 if (exists("singlefile_galaxyPaths")){
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541 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,","))
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542 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,","))
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543
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544 singlefile <- NULL
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545 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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546 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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547 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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548 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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549 }
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550 }
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551 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
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552 args[[argument]] <- NULL
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553 }
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554 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
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555 }
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556
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557
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558 # This function retrieve the raw file in the working directory
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559 # - if zipfile: unzip the file with its directory tree
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560 # - if singlefiles: set symlink with the good filename
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561 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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562 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
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lecorguille
parents: 20
diff changeset
563 if(!is.null(singlefile) && (length("singlefile")>0)) {
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lecorguille
parents: 20
diff changeset
564 for (singlefile_sampleName in names(singlefile)) {
31
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lecorguille
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diff changeset
565 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
23
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lecorguille
parents: 20
diff changeset
566 if(!file.exists(singlefile_galaxyPath)){
31
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lecorguille
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diff changeset
567 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
23
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lecorguille
parents: 20
diff changeset
568 print(error_message); stop(error_message)
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lecorguille
parents: 20
diff changeset
569 }
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lecorguille
parents: 20
diff changeset
570
31
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lecorguille
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diff changeset
571 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
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lecorguille
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diff changeset
572 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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lecorguille
parents: 30
diff changeset
573
23
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lecorguille
parents: 20
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574 }
31
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lecorguille
parents: 30
diff changeset
575 directory <- "."
23
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lecorguille
parents: 20
diff changeset
576
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lecorguille
parents: 20
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577 }
31
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lecorguille
parents: 30
diff changeset
578 if(!is.null(zipfile) && (zipfile != "")) {
23
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lecorguille
parents: 20
diff changeset
579 if(!file.exists(zipfile)){
31
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lecorguille
parents: 30
diff changeset
580 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
23
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lecorguille
parents: 20
diff changeset
581 print(error_message)
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 20
diff changeset
582 stop(error_message)
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 20
diff changeset
583 }
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lecorguille
parents: 20
diff changeset
584
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lecorguille
parents: 20
diff changeset
585 #list all file in the zip file
31
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lecorguille
parents: 30
diff changeset
586 #zip_files <- unzip(zipfile,list=T)[,"Name"]
23
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lecorguille
parents: 20
diff changeset
587
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 20
diff changeset
588 #unzip
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lecorguille
parents: 20
diff changeset
589 suppressWarnings(unzip(zipfile, unzip="unzip"))
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lecorguille
parents: 20
diff changeset
590
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lecorguille
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diff changeset
591 #get the directory name
31
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lecorguille
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diff changeset
592 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
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lecorguille
parents: 30
diff changeset
593 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
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lecorguille
parents: 30
diff changeset
594 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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lecorguille
parents: 30
diff changeset
595 directory <- "."
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lecorguille
parents: 30
diff changeset
596 if (length(directories) == 1) directory <- directories
23
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lecorguille
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diff changeset
597
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lecorguille
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diff changeset
598 cat("files_root_directory\t",directory,"\n")
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lecorguille
parents: 20
diff changeset
599
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lecorguille
parents: 20
diff changeset
600 }
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lecorguille
parents: 20
diff changeset
601 return (directory)
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lecorguille
parents: 20
diff changeset
602 }
31
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lecorguille
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diff changeset
603
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lecorguille
parents: 30
diff changeset
604
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lecorguille
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diff changeset
605 # This function retrieve a xset like object
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lecorguille
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diff changeset
606 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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lecorguille
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diff changeset
607 getxcmsSetObject <- function(xobject) {
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lecorguille
parents: 30
diff changeset
608 # XCMS 1.x
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lecorguille
parents: 30
diff changeset
609 if (class(xobject) == "xcmsSet")
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lecorguille
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diff changeset
610 return (xobject)
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lecorguille
parents: 30
diff changeset
611 # XCMS 3.x
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lecorguille
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612 if (class(xobject) == "XCMSnExp") {
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lecorguille
parents: 30
diff changeset
613 # Get the legacy xcmsSet object
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diff changeset
614 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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lecorguille
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diff changeset
615 sampclass(xset) <- xset@phenoData$sample_group
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lecorguille
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diff changeset
616 return (xset)
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lecorguille
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diff changeset
617 }
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lecorguille
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diff changeset
618 }
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lecorguille
parents: 30
diff changeset
619
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lecorguille
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diff changeset
620
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lecorguille
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diff changeset
621 #@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
diff changeset
622 # https://github.com/sneumann/xcms/issues/250
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lecorguille
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diff changeset
623 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
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lecorguille
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diff changeset
624 mzfmt <- paste("%.", mzdec, "f", sep = "")
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lecorguille
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diff changeset
625 rtfmt <- paste("%.", rtdec, "f", sep = "")
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lecorguille
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diff changeset
626
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diff changeset
627 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
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lecorguille
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diff changeset
628 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
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lecorguille
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diff changeset
629
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lecorguille
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diff changeset
630 if (any(dup <- duplicated(gnames)))
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lecorguille
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diff changeset
631 for (dupname in unique(gnames[dup])) {
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lecorguille
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diff changeset
632 dupidx <- which(gnames == dupname)
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lecorguille
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diff changeset
633 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
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lecorguille
parents: 30
diff changeset
634 }
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lecorguille
parents: 30
diff changeset
635
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lecorguille
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diff changeset
636 return (gnames)
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lecorguille
parents: 30
diff changeset
637 }
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lecorguille
parents: 30
diff changeset
638
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lecorguille
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diff changeset
639 #@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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diff changeset
640 # https://github.com/sneumann/xcms/issues/247
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lecorguille
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diff changeset
641 .concatenate_XCMSnExp <- function(...) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
642 x <- list(...)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
643 if (length(x) == 0)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
644 return(NULL)
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lecorguille
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diff changeset
645 if (length(x) == 1)
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lecorguille
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diff changeset
646 return(x[[1]])
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lecorguille
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diff changeset
647 ## Check that all are XCMSnExp objects.
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lecorguille
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diff changeset
648 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
649 stop("All passed objects should be 'XCMSnExp' objects")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
650 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
651 ## If any of the XCMSnExp has alignment results or detected features drop
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lecorguille
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diff changeset
652 ## them!
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lecorguille
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diff changeset
653 x <- lapply(x, function(z) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
654 if (hasAdjustedRtime(z)) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
655 z <- dropAdjustedRtime(z)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
656 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
657 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
658 if (hasFeatures(z)) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
659 z <- dropFeatureDefinitions(z)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
660 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
661 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
662 z
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 ## Combine peaks
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
665 fls <- lapply(x, fileNames)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
666 startidx <- cumsum(lengths(fls))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
667 pks <- lapply(x, chromPeaks)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
668 procH <- lapply(x, processHistory)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
669 for (i in 2:length(fls)) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
670 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
671 procH[[i]] <- lapply(procH[[i]], function(z) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
672 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
673 z
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
674 })
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
675 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
676 pks <- do.call(rbind, pks)
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lecorguille
parents: 30
diff changeset
677 new_x@.processHistory <- unlist(procH)
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lecorguille
parents: 30
diff changeset
678 chromPeaks(new_x) <- pks
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
679 if (validObject(new_x))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
680 new_x
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lecorguille
parents: 30
diff changeset
681 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
682
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
683 #@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
diff changeset
684 # https://github.com/sneumann/xcms/issues/247
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lecorguille
parents: 30
diff changeset
685 .concatenate_OnDiskMSnExp <- function(...) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
686 x <- list(...)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
687 if (length(x) == 0)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
688 return(NULL)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
689 if (length(x) == 1)
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lecorguille
parents: 30
diff changeset
690 return(x[[1]])
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lecorguille
parents: 30
diff changeset
691 ## Check that all are XCMSnExp objects.
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
692 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
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lecorguille
parents: 30
diff changeset
693 stop("All passed objects should be 'OnDiskMSnExp' objects")
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lecorguille
parents: 30
diff changeset
694 ## Check processingQueue
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lecorguille
parents: 30
diff changeset
695 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
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lecorguille
parents: 30
diff changeset
696 new_procQ <- procQ[[1]]
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lecorguille
parents: 30
diff changeset
697 is_ok <- unlist(lapply(procQ, function(z)
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lecorguille
parents: 30
diff changeset
698 !is.character(all.equal(new_procQ, z))
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lecorguille
parents: 30
diff changeset
699 ))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
700 if (any(!is_ok)) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
701 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
702 "Dropping the processing queue.")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
703 new_procQ <- list()
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
704 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
705 ## processingData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
706 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
707 startidx <- cumsum(lengths(fls))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
708 ## featureData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
709 featd <- lapply(x, fData)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
710 ## 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
711 for (i in 2:length(featd)) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
712 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
713 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
714 fileIds = featd[[i]]$fileIdx,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
715 spectrumIds = featd[[i]]$spIdx,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
716 nSpectra = nrow(featd[[i]]),
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
717 nFiles = length(unlist(fls))
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lecorguille
parents: 30
diff changeset
718 )
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
719 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
720 featd <- do.call(rbind, featd)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
721 featd$spectrum <- 1:nrow(featd)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
722 ## experimentData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
723 expdata <- lapply(x, function(z) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
724 ed <- z@experimentData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
725 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
726 instrumentModel = ed@instrumentModel,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
727 ionSource = ed@ionSource,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
728 analyser = ed@analyser,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
729 detectorType = ed@detectorType,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
730 stringsAsFactors = FALSE)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
731 })
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
732 expdata <- do.call(rbind, expdata)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
733 expdata <- new("MIAPE",
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
734 instrumentManufacturer = expdata$instrumentManufacturer,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
735 instrumentModel = expdata$instrumentModel,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
736 ionSource = expdata$ionSource,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
737 analyser = expdata$analyser,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
738 detectorType = expdata$detectorType)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
739
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
740 ## protocolData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
741 protodata <- lapply(x, function(z) z@protocolData)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
742 if (any(unlist(lapply(protodata, nrow)) > 0))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
743 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
744 " currently not supported. Skipped.")
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
745 ## phenoData
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
746 pdata <- do.call(rbind, lapply(x, pData))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
747 res <- new(
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
748 "OnDiskMSnExp",
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
749 phenoData = new("NAnnotatedDataFrame", data = pdata),
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
750 featureData = new("AnnotatedDataFrame", featd),
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
751 processingData = new("MSnProcess",
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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752 processing = paste0("Concatenated [", date(), "]"),
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
753 files = unlist(fls), smoothed = NA),
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
754 experimentData = expdata,
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
755 spectraProcessingQueue = new_procQ)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
756 if (validObject(res))
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
757 res
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
758 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
759
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
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760 #@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
761 # https://github.com/sneumann/xcms/issues/247
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
762 c.XCMSnExp <- function(...) {
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
763 .concatenate_XCMSnExp(...)
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
764 }