Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate lib.r @ 6:e0b5c547925d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
author lecorguille
date Wed, 05 Sep 2018 05:57:13 -0400
parents a5ba342e72e0
children a4a1143a202a
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fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
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1 #@authors ABiMS TEAM, Y. Guitton
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lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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lecorguille
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4 #@author G. Le Corguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
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lecorguille
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6 parseCommandArgs <- function(...) {
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7 args <- batch::parseCommandArgs(...)
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8 for (key in names(args)) {
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9 if (args[key] %in% c("TRUE","FALSE"))
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10 args[key] = as.logical(args[key])
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11 }
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12 return(args)
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13 }
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15 #@author G. Le Corguille
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16 # This function will
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
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17 # - load the packages
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18 # - display the sessionInfo
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19 loadAndDisplayPackages <- function(pkgs) {
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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22 sessioninfo = sessionInfo()
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23 cat(sessioninfo$R.version$version.string,"\n")
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24 cat("Main packages:\n")
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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26 cat("Other loaded packages:\n")
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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28 }
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30 #@author G. Le Corguille
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31 # This function merge several chromBPI or chromTIC into one.
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32 mergeChrom <- function(chrom_merged, chrom) {
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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33 if (is.null(chrom_merged)) return(NULL)
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
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35 return(chrom_merged)
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36 }
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38 #@author G. Le Corguille
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lecorguille
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39 # This function merge several xdata into one.
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40 mergeXData <- function(args) {
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lecorguille
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41 chromTIC <- NULL
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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42 chromBPI <- NULL
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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43 chromTIC_adjusted <- NULL
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44 chromBPI_adjusted <- NULL
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45 for(image in args$images) {
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46
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47 load(image)
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lecorguille
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48 # Handle infiles
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lecorguille
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49 if (!exists("singlefile")) singlefile <- NULL
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50 if (!exists("zipfile")) zipfile <- NULL
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51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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lecorguille
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52 zipfile <- rawFilePath$zipfile
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53 singlefile <- rawFilePath$singlefile
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54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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55
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56 if (exists("raw_data")) xdata <- raw_data
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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58
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59 cat(sampleNamesList$sampleNamesOrigin,"\n")
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60
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61 if (!exists("xdata_merged")) {
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62 xdata_merged <- xdata
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63 singlefile_merged <- singlefile
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lecorguille
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64 md5sumList_merged <- md5sumList
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65 sampleNamesList_merged <- sampleNamesList
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66 chromTIC_merged <- chromTIC
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67 chromBPI_merged <- chromBPI
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lecorguille
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68 chromTIC_adjusted_merged <- chromTIC_adjusted
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69 chromBPI_adjusted_merged <- chromBPI_adjusted
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70 } else {
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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74
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75 singlefile_merged <- c(singlefile_merged,singlefile)
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lecorguille
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
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lecorguille
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
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lecorguille
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
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lecorguille
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
e0b5c547925d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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83 }
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84 }
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85 rm(image)
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lecorguille
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86 xdata <- xdata_merged; rm(xdata_merged)
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87 singlefile <- singlefile_merged; rm(singlefile_merged)
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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90
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91 if (!is.null(args$sampleMetadata)) {
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92 cat("\tXSET PHENODATA SETTING...\n")
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93 sampleMetadataFile <- args$sampleMetadata
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
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96
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97 if (any(is.na(pData(xdata)$sample_group))) {
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
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100 print(error_message)
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101 stop(error_message)
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102 }
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103 }
6
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104
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
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107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
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108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
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109
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110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
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111 }
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112
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113 #@author G. Le Corguille
0
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114 # This function convert if it is required the Retention Time in minutes
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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116 if (convertRTMinute){
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117 #converting the retention times (seconds) into minutes
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118 print("converting the retention times into minutes in the variableMetadata")
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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122 }
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123 return (variableMetadata)
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124 }
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125
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126 #@author G. Le Corguille
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127 # This function format ions identifiers
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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133 return(variableMetadata)
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134 }
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135
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136 #@author G. Le Corguille
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137 # Draw the plotChromPeakDensity 3 per page in a pdf file
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138 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
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139 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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140
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141 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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142
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143 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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144 names(group_colors) <- unique(xdata$sample_group)
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145
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146 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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147 for (i in 1:nrow(featureDefinitions(xdata))) {
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148 mzmin = featureDefinitions(xdata)[i,]$mzmin
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149 mzmax = featureDefinitions(xdata)[i,]$mzmax
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150 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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151 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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152 }
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153
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154 dev.off()
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155 }
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156
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157 #@author G. Le Corguille
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158 # Draw the plotChromPeakDensity 3 per page in a pdf file
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159 getPlotAdjustedRtime <- function(xdata) {
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160
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161 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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162
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163 # Color by group
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164 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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165 if (length(group_colors) > 1) {
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166 names(group_colors) <- unique(xdata$sample_group)
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167 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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168 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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169 }
0
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170
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171 # Color by sample
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172 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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173 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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174
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175 dev.off()
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176 }
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177
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178 #@author G. Le Corguille
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179 # value: intensity values to be used into, maxo or intb
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180 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
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181 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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182 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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183 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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184 variableMetadata <- featureDefinitions(xdata)
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185 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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186 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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187
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188 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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189 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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190
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191 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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192 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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193
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194 }
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195
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196 #@author G. Le Corguille
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197 # It allow different of field separators
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198 getDataFrameFromFile <- function(filename, header=T) {
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199 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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200 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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201 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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202 if (ncol(myDataFrame) < 2) {
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203 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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204 print(error_message)
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205 stop(error_message)
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206 }
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207 return(myDataFrame)
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208 }
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209
6
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210 #@author G. Le Corguille
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211 # Draw the BPI and TIC graphics
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212 # colored by sample names or class names
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213 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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214
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215 if (aggregationFun == "sum")
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216 type="Total Ion Chromatograms"
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217 else
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218 type="Base Peak Intensity Chromatograms"
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219
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220 adjusted="Raw"
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221 if (hasAdjustedRtime(xdata))
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222 adjusted="Adjusted"
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223
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224 main <- paste(type,":",adjusted,"data")
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225
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226 pdf(pdfname, width=16, height=10)
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227
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228 # Color by group
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229 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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230 if (length(group_colors) > 1) {
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231 names(group_colors) <- unique(xdata$sample_group)
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232 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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233 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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234 }
0
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235
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236 # Color by sample
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237 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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238 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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239
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240 dev.off()
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241 }
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242
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243
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244 # Get the polarities from all the samples of a condition
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245 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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246 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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247 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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248 cat("Creating the sampleMetadata file...\n")
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249
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250 #Create the sampleMetada dataframe
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251 sampleMetadata <- xdata@phenoData@data
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252 rownames(sampleMetadata) <- NULL
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253 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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254
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255 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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256 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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257
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258 if (any(duplicated(sampleNamesMakeNames))) {
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259 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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260 for (sampleName in sampleNamesOrigin) {
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261 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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262 }
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263 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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264 }
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265
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266 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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267 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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268 for (sampleName in sampleNamesOrigin) {
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269 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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270 }
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271 }
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272
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273 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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274
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275
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276 #For each sample file, the following actions are done
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277 for (fileIdx in 1:length(fileNames(xdata))) {
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278 #Check if the file is in the CDF format
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279 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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280
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281 # If the column isn't exist, with add one filled with NA
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282 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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283
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284 #Extract the polarity (a list of polarities)
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285 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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286 #Verify if all the scans have the same polarity
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287 uniq_list <- unique(polarity)
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288 if (length(uniq_list)>1){
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289 polarity <- "mixed"
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290 } else {
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291 polarity <- as.character(uniq_list)
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292 }
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293
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294 #Set the polarity attribute
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295 sampleMetadata$polarity[fileIdx] <- polarity
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296 }
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297
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298 }
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299
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300 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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301
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302 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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303
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304 }
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305
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306
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307 # This function check if xcms will found all the files
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308 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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309 checkFilesCompatibilityWithXcms <- function(directory) {
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310 cat("Checking files filenames compatibilities with xmcs...\n")
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311 # WHAT XCMS WILL FIND
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312 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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313 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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314 info <- file.info(directory)
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315 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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316 files <- c(directory[!info$isdir], listed)
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317 files_abs <- file.path(getwd(), files)
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318 exists <- file.exists(files_abs)
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319 files[exists] <- files_abs[exists]
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320 files[exists] <- sub("//","/",files[exists])
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321
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322 # WHAT IS ON THE FILESYSTEM
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323 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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324 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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325
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326 # COMPARISON
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327 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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328 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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329 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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330 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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331 }
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332 }
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333
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334
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335 #This function list the compatible files within the directory as xcms did
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336 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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337 getMSFiles <- function (directory) {
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338 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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339 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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340 info <- file.info(directory)
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341 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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342 files <- c(directory[!info$isdir], listed)
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343 exists <- file.exists(files)
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344 files <- files[exists]
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345 return(files)
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346 }
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347
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348 # This function check if XML contains special caracters. It also checks integrity and completness.
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349 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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350 checkXmlStructure <- function (directory) {
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351 cat("Checking XML structure...\n")
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352
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353 cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
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354 capture <- system(cmd, intern=TRUE)
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355
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356 if (length(capture)>0){
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357 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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358 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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359 write(capture, stderr())
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360 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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361 }
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362
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363 }
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364
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365
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366 # This function check if XML contain special characters
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367 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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368 deleteXmlBadCharacters<- function (directory) {
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369 cat("Checking Non ASCII characters in the XML...\n")
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370
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371 processed <- F
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372 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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373 for (i in l){
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374 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
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375 capture <- suppressWarnings(system(cmd, intern=TRUE))
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376 if (length(capture)>0){
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377 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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378 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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379 c <- system(cmd, intern=TRUE)
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380 capture <- ""
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381 processed <- T
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382 }
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383 }
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384 if (processed) cat("\n\n")
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385 return(processed)
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386 }
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387
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388
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389 # This function will compute MD5 checksum to check the data integrity
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390 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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391 getMd5sum <- function (directory) {
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392 cat("Compute md5 checksum...\n")
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393 # WHAT XCMS WILL FIND
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394 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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395 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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396 info <- file.info(directory)
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397 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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398 files <- c(directory[!info$isdir], listed)
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399 exists <- file.exists(files)
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400 files <- files[exists]
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401
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402 library(tools)
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403
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404 #cat("\n\n")
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405
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406 return(as.matrix(md5sum(files)))
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407 }
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408
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409
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410 # This function get the raw file path from the arguments
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411 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
5
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412 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
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413 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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414
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415 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
0
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416
5
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417 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
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418 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
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419 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
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420 }
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421 if (exists("singlefile_galaxyPaths")){
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422 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
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423 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
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424
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425 singlefile <- NULL
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426 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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427 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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428 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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429 # In case, an url is used to import data within Galaxy
5
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430 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
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431 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
0
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432 }
5
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433 }
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434 return(list(zipfile=zipfile, singlefile=singlefile))
0
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435 }
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436
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437 # This function retrieve the raw file in the working directory
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438 # - if zipfile: unzip the file with its directory tree
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439 # - if singlefiles: set symlink with the good filename
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440 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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441 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
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442 if(!is.null(singlefile) && (length("singlefile")>0)) {
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443 for (singlefile_sampleName in names(singlefile)) {
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444 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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lecorguille
parents:
diff changeset
445 if(!file.exists(singlefile_galaxyPath)){
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lecorguille
parents:
diff changeset
446 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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lecorguille
parents:
diff changeset
447 print(error_message); stop(error_message)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
448 }
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lecorguille
parents:
diff changeset
449
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lecorguille
parents:
diff changeset
450 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
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lecorguille
parents:
diff changeset
451 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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lecorguille
parents:
diff changeset
452
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lecorguille
parents:
diff changeset
453 }
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lecorguille
parents:
diff changeset
454 directory <- "."
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
455
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lecorguille
parents:
diff changeset
456 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
457 if(!is.null(zipfile) && (zipfile != "")) {
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lecorguille
parents:
diff changeset
458 if(!file.exists(zipfile)){
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lecorguille
parents:
diff changeset
459 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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lecorguille
parents:
diff changeset
460 print(error_message)
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lecorguille
parents:
diff changeset
461 stop(error_message)
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lecorguille
parents:
diff changeset
462 }
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lecorguille
parents:
diff changeset
463
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lecorguille
parents:
diff changeset
464 #list all file in the zip file
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lecorguille
parents:
diff changeset
465 #zip_files <- unzip(zipfile,list=T)[,"Name"]
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lecorguille
parents:
diff changeset
466
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lecorguille
parents:
diff changeset
467 #unzip
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
468 suppressWarnings(unzip(zipfile, unzip="unzip"))
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lecorguille
parents:
diff changeset
469
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lecorguille
parents:
diff changeset
470 #get the directory name
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
471 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
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lecorguille
parents:
diff changeset
472 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
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lecorguille
parents:
diff changeset
473 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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lecorguille
parents:
diff changeset
474 directory <- "."
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
475 if (length(directories) == 1) directory <- directories
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
476
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
477 cat("files_root_directory\t",directory,"\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
478
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lecorguille
parents:
diff changeset
479 }
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lecorguille
parents:
diff changeset
480 return (directory)
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lecorguille
parents:
diff changeset
481 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
482
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
483
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
484 # This function retrieve a xset like object
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
485 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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lecorguille
parents:
diff changeset
486 getxcmsSetObject <- function(xobject) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
487 # XCMS 1.x
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lecorguille
parents:
diff changeset
488 if (class(xobject) == "xcmsSet")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
489 return (xobject)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
490 # XCMS 3.x
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lecorguille
parents:
diff changeset
491 if (class(xobject) == "XCMSnExp") {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
492 # Get the legacy xcmsSet object
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
493 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
5
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lecorguille
parents: 3
diff changeset
494 if (!is.null(xset@phenoData$sample_group))
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lecorguille
parents: 3
diff changeset
495 sampclass(xset) <- xset@phenoData$sample_group
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lecorguille
parents: 3
diff changeset
496 else
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lecorguille
parents: 3
diff changeset
497 sampclass(xset) <- "."
0
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lecorguille
parents:
diff changeset
498 return (xset)
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lecorguille
parents:
diff changeset
499 }
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lecorguille
parents:
diff changeset
500 }
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lecorguille
parents:
diff changeset
501
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lecorguille
parents:
diff changeset
502
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
503 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
504 # https://github.com/sneumann/xcms/issues/250
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lecorguille
parents:
diff changeset
505 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
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lecorguille
parents:
diff changeset
506 mzfmt <- paste("%.", mzdec, "f", sep = "")
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lecorguille
parents:
diff changeset
507 rtfmt <- paste("%.", rtdec, "f", sep = "")
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lecorguille
parents:
diff changeset
508
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lecorguille
parents:
diff changeset
509 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
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lecorguille
parents:
diff changeset
510 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
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lecorguille
parents:
diff changeset
511
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lecorguille
parents:
diff changeset
512 if (any(dup <- duplicated(gnames)))
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lecorguille
parents:
diff changeset
513 for (dupname in unique(gnames[dup])) {
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lecorguille
parents:
diff changeset
514 dupidx <- which(gnames == dupname)
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lecorguille
parents:
diff changeset
515 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
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lecorguille
parents:
diff changeset
516 }
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lecorguille
parents:
diff changeset
517
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lecorguille
parents:
diff changeset
518 return (gnames)
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lecorguille
parents:
diff changeset
519 }
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lecorguille
parents:
diff changeset
520
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lecorguille
parents:
diff changeset
521 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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lecorguille
parents:
diff changeset
522 # https://github.com/sneumann/xcms/issues/247
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lecorguille
parents:
diff changeset
523 .concatenate_XCMSnExp <- function(...) {
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lecorguille
parents:
diff changeset
524 x <- list(...)
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lecorguille
parents:
diff changeset
525 if (length(x) == 0)
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lecorguille
parents:
diff changeset
526 return(NULL)
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lecorguille
parents:
diff changeset
527 if (length(x) == 1)
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lecorguille
parents:
diff changeset
528 return(x[[1]])
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lecorguille
parents:
diff changeset
529 ## Check that all are XCMSnExp objects.
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lecorguille
parents:
diff changeset
530 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
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lecorguille
parents:
diff changeset
531 stop("All passed objects should be 'XCMSnExp' objects")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
532 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
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lecorguille
parents:
diff changeset
533 ## If any of the XCMSnExp has alignment results or detected features drop
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lecorguille
parents:
diff changeset
534 ## them!
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lecorguille
parents:
diff changeset
535 x <- lapply(x, function(z) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
536 if (hasAdjustedRtime(z)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
537 z <- dropAdjustedRtime(z)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
538 warning("Adjusted retention times found, had to drop them.")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
539 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
540 if (hasFeatures(z)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
541 z <- dropFeatureDefinitions(z)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
542 warning("Feature definitions found, had to drop them.")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
543 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
544 z
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
545 })
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
546 ## Combine peaks
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
547 fls <- lapply(x, fileNames)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
548 startidx <- cumsum(lengths(fls))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
549 pks <- lapply(x, chromPeaks)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
550 procH <- lapply(x, processHistory)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
551 for (i in 2:length(fls)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
552 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
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lecorguille
parents:
diff changeset
553 procH[[i]] <- lapply(procH[[i]], function(z) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
554 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
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lecorguille
parents:
diff changeset
555 z
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
556 })
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lecorguille
parents:
diff changeset
557 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
558 pks <- do.call(rbind, pks)
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lecorguille
parents:
diff changeset
559 new_x@.processHistory <- unlist(procH)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
560 chromPeaks(new_x) <- pks
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
561 if (validObject(new_x))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
562 new_x
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
563 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
564
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
565 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
566 # https://github.com/sneumann/xcms/issues/247
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
567 .concatenate_OnDiskMSnExp <- function(...) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
568 x <- list(...)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
569 if (length(x) == 0)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
570 return(NULL)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
571 if (length(x) == 1)
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lecorguille
parents:
diff changeset
572 return(x[[1]])
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
573 ## Check that all are XCMSnExp objects.
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lecorguille
parents:
diff changeset
574 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
575 stop("All passed objects should be 'OnDiskMSnExp' objects")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
576 ## Check processingQueue
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
577 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
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lecorguille
parents:
diff changeset
578 new_procQ <- procQ[[1]]
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lecorguille
parents:
diff changeset
579 is_ok <- unlist(lapply(procQ, function(z)
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lecorguille
parents:
diff changeset
580 !is.character(all.equal(new_procQ, z))
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lecorguille
parents:
diff changeset
581 ))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
582 if (any(!is_ok)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
583 warning("Processing queues from the submitted objects differ! ",
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
584 "Dropping the processing queue.")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
585 new_procQ <- list()
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
586 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
587 ## processingData
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
588 fls <- lapply(x, function(z) z@processingData@files)
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lecorguille
parents:
diff changeset
589 startidx <- cumsum(lengths(fls))
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lecorguille
parents:
diff changeset
590 ## featureData
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
591 featd <- lapply(x, fData)
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lecorguille
parents:
diff changeset
592 ## Have to update the file index and the spectrum names.
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
593 for (i in 2:length(featd)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
594 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
595 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
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lecorguille
parents:
diff changeset
596 fileIds = featd[[i]]$fileIdx,
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lecorguille
parents:
diff changeset
597 spectrumIds = featd[[i]]$spIdx,
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lecorguille
parents:
diff changeset
598 nSpectra = nrow(featd[[i]]),
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lecorguille
parents:
diff changeset
599 nFiles = length(unlist(fls))
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lecorguille
parents:
diff changeset
600 )
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
601 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
602 featd <- do.call(rbind, featd)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
603 featd$spectrum <- 1:nrow(featd)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
604 ## experimentData
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
605 expdata <- lapply(x, function(z) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
606 ed <- z@experimentData
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
607 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
608 instrumentModel = ed@instrumentModel,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
609 ionSource = ed@ionSource,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
610 analyser = ed@analyser,
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lecorguille
parents:
diff changeset
611 detectorType = ed@detectorType,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
612 stringsAsFactors = FALSE)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
613 })
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
614 expdata <- do.call(rbind, expdata)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
615 expdata <- new("MIAPE",
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lecorguille
parents:
diff changeset
616 instrumentManufacturer = expdata$instrumentManufacturer,
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lecorguille
parents:
diff changeset
617 instrumentModel = expdata$instrumentModel,
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lecorguille
parents:
diff changeset
618 ionSource = expdata$ionSource,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
619 analyser = expdata$analyser,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
620 detectorType = expdata$detectorType)
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lecorguille
parents:
diff changeset
621
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
622 ## protocolData
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
diff changeset
623 protodata <- lapply(x, function(z) z@protocolData)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty
lecorguille
parents:
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624 if (any(unlist(lapply(protodata, nrow)) > 0))
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625 warning("Found non-empty protocol data, but merging protocol data is",
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626 " currently not supported. Skipped.")
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627 ## phenoData
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628 pdata <- do.call(rbind, lapply(x, pData))
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629 res <- new(
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630 "OnDiskMSnExp",
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631 phenoData = new("NAnnotatedDataFrame", data = pdata),
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632 featureData = new("AnnotatedDataFrame", featd),
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633 processingData = new("MSnProcess",
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634 processing = paste0("Concatenated [", date(), "]"),
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635 files = unlist(fls), smoothed = NA),
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636 experimentData = expdata,
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637 spectraProcessingQueue = new_procQ)
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638 if (validObject(res))
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639 res
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640 }
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641
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642 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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643 # https://github.com/sneumann/xcms/issues/247
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644 c.XCMSnExp <- function(...) {
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645 .concatenate_XCMSnExp(...)
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646 }
2
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647
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648 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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649 # https://github.com/sneumann/xcms/issues/247
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650 c.MSnbase <- function(...) {
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651 .concatenate_OnDiskMSnExp(...)
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652 }