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annotate lib.r @ 28:2b676d5eb848 draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:16:31 +0000
parents d45a786cbc40
children
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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1 #@authors ABiMS TEAM, Y. Guitton
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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4 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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6 parseCommandArgs <- function(...) {
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2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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7 args <- batch::parseCommandArgs(...)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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8 for (key in names(args)) {
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9 if (args[key] %in% c("TRUE", "FALSE"))
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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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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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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13 }
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2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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15 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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16 # This function will
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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17 # - load the packages
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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18 # - display the sessionInfo
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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22 sessioninfo <- sessionInfo()
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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23 cat(sessioninfo$R.version$version.string, "\n")
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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24 cat("Main packages:\n")
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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25 for (pkg in names(sessioninfo$otherPkgs)) {
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26 cat(paste(pkg, packageVersion(pkg)), "\t")
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27 }
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28 cat("\n")
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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29 cat("Other loaded packages:\n")
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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30 for (pkg in names(sessioninfo$loadedOnly)) {
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31 cat(paste(pkg, packageVersion(pkg)), "\t")
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32 }
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33 cat("\n")
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34 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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36 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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37 # This function merge several chromBPI or chromTIC into one.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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38 mergeChrom <- function(chrom_merged, chrom) {
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39 if (is.null(chrom_merged)) return(NULL)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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40 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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41 return(chrom_merged)
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42 }
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44 #@author G. Le Corguille
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45 # This function merge several xdata into one.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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46 mergeXData <- function(args) {
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47 chromTIC <- NULL
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48 chromBPI <- NULL
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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49 chromTIC_adjusted <- NULL
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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50 chromBPI_adjusted <- NULL
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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51 md5sumList <- NULL
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52 for (image in args$images) {
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54 load(image)
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55 # Handle infiles
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56 if (!exists("singlefile")) singlefile <- NULL
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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57 if (!exists("zipfile")) zipfile <- NULL
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58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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59 zipfile <- rawFilePath$zipfile
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60 singlefile <- rawFilePath$singlefile
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61
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62 if (exists("raw_data")) xdata <- raw_data
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63 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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64
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65 cat(sampleNamesList$sampleNamesOrigin, "\n")
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66
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67 if (!exists("xdata_merged")) {
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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68 xdata_merged <- xdata
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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69 singlefile_merged <- singlefile
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70 md5sumList_merged <- md5sumList
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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71 sampleNamesList_merged <- sampleNamesList
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72 chromTIC_merged <- chromTIC
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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73 chromBPI_merged <- chromBPI
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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74 chromTIC_adjusted_merged <- chromTIC_adjusted
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75 chromBPI_adjusted_merged <- chromBPI_adjusted
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76 } else {
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77 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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78 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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79 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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80
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81 singlefile_merged <- c(singlefile_merged, singlefile)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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82 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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83 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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84 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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85 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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86 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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87 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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88 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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89 }
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90 }
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91 rm(image)
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92 xdata <- xdata_merged
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93 rm(xdata_merged)
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94 singlefile <- singlefile_merged
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95 rm(singlefile_merged)
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96 md5sumList <- md5sumList_merged
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97 rm(md5sumList_merged)
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98 sampleNamesList <- sampleNamesList_merged
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99 rm(sampleNamesList_merged)
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100
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101 if (!is.null(args$sampleMetadata)) {
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102 cat("\tXSET PHENODATA SETTING...\n")
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103 sampleMetadataFile <- args$sampleMetadata
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104 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = FALSE)
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105 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
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106
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107 if (any(is.na(pData(xdata)$sample_group))) {
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108 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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109 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " "))
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110 print(error_message)
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111 stop(error_message)
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112 }
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113 }
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114
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115 if (!is.null(chromTIC_merged)) {
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116 chromTIC <- chromTIC_merged
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117 chromTIC@phenoData <- xdata@phenoData
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118 }
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119 if (!is.null(chromBPI_merged)) {
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120 chromBPI <- chromBPI_merged
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121 chromBPI@phenoData <- xdata@phenoData
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122 }
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123 if (!is.null(chromTIC_adjusted_merged)) {
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124 chromTIC_adjusted <- chromTIC_adjusted_merged
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125 chromTIC_adjusted@phenoData <- xdata@phenoData
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126 }
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127 if (!is.null(chromBPI_adjusted_merged)) {
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128 chromBPI_adjusted <- chromBPI_adjusted_merged
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129 chromBPI_adjusted@phenoData <- xdata@phenoData
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130 }
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131
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132 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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133 }
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134
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135 #@author G. Le Corguille
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136 # This function convert if it is required the Retention Time in minutes
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137 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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138 if (convertRTMinute) {
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139 #converting the retention times (seconds) into minutes
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140 print("converting the retention times into minutes in the variableMetadata")
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141 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
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142 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
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143 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
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144 }
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145 return(variableMetadata)
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146 }
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147
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148 #@author G. Le Corguille
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149 # This function format ions identifiers
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150 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
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151 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
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152 idsDeco <- sapply(splitDeco,
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153 function(x) {
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154 deco <- unlist(x)[2]
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155 if (is.na(deco)) return("") else return(paste0("_", deco))
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156 }
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157 )
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158 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
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159 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
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160 return(variableMetadata)
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161 }
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162
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163 #@author G. Le Corguille
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164 # This function convert the remain NA to 0 in the dataMatrix
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165 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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166 if (naTOzero) {
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167 dataMatrix[is.na(dataMatrix)] <- 0
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168 }
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169 return(dataMatrix)
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170 }
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171
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172 #@author G. Le Corguille
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173 # Draw the plotChromPeakDensity 3 per page in a pdf file
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174 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
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175 pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
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176
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177 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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178
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179 if (length(unique(xdata$sample_group)) < 10) {
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180 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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181 } else {
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182 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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183 }
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184 names(group_colors) <- unique(xdata$sample_group)
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185 col_per_samp <- as.character(xdata$sample_group)
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186 for (i in seq_len(length(group_colors))) {
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187 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
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188 }
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189
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190 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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191 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
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192 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
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193 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
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194 plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
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195 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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196 }
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197
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198 dev.off()
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199 }
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200
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201 #@author G. Le Corguille
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202 # Draw the plotChromPeakDensity 3 per page in a pdf file
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203 getPlotAdjustedRtime <- function(xdata) {
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204
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205 pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
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206
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207 # Color by group
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208 if (length(unique(xdata$sample_group)) < 10) {
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209 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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210 } else {
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211 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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212 }
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213 if (length(group_colors) > 1) {
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214 names(group_colors) <- unique(xdata$sample_group)
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215 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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216 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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217 }
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218
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219 # Color by sample
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220 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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221 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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222
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223 dev.off()
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224 }
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225
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226 #@author G. Le Corguille
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227 # value: intensity values to be used into, maxo or intb
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228 getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = FALSE, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = TRUE, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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229 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
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230 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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231 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
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232 variableMetadata <- featureDefinitions(xdata)
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233 colnames(variableMetadata)[1] <- "mz"
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234 colnames(variableMetadata)[4] <- "rt"
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235 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
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236
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237 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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238 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
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239 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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240
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241 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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242 variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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243
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244 write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = FALSE, row.names = FALSE)
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245 write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = FALSE, row.names = FALSE)
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246
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247 }
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248
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249 #@author G. Le Corguille
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250 # It allow different of field separators
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251 getDataFrameFromFile <- function(filename, header = TRUE) {
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252 myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = FALSE)
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253 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = FALSE)
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254 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = FALSE)
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255 if (ncol(myDataFrame) < 2) {
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256 error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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257 print(error_message)
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258 stop(error_message)
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259 }
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260 return(myDataFrame)
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261 }
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262
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263 #@author G. Le Corguille
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264 # Draw the BPI and TIC graphics
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265 # colored by sample names or class names
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266 getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
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267
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268 if (aggregationFun == "sum")
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269 type <- "Total Ion Chromatograms"
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270 else
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271 type <- "Base Peak Intensity Chromatograms"
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272
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273 adjusted <- "Raw"
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274 if (hasAdjustedRtime(xdata))
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275 adjusted <- "Adjusted"
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276
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277 main <- paste(type, ":", adjusted, "data")
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278
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279 pdf(pdfname, width = 16, height = 10)
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280
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281 # Color by group
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282 if (length(unique(xdata$sample_group)) < 10) {
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283 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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284 } else {
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285 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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286 }
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287 if (length(group_colors) > 1) {
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288 names(group_colors) <- unique(xdata$sample_group)
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289 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
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290 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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291 }
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292
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293 # Color by sample
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294 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
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295 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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296
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297 dev.off()
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298 }
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299
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300
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301 # Get the polarities from all the samples of a condition
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302 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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303 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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304 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
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305 cat("Creating the sampleMetadata file...\n")
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306
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307 #Create the sampleMetada dataframe
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308 sampleMetadata <- xdata@phenoData@data
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309 rownames(sampleMetadata) <- NULL
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310 colnames(sampleMetadata) <- c("sample_name", "class")
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311
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312 sampleNamesOrigin <- sampleMetadata$sample_name
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313 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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314
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315 if (any(duplicated(sampleNamesMakeNames))) {
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316 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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317 for (sampleName in sampleNamesOrigin) {
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318 write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
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319 }
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320 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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321 }
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322
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323 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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324 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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325 for (sampleName in sampleNamesOrigin) {
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326 cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
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327 }
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328 }
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329
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330 sampleMetadata$sample_name <- sampleNamesMakeNames
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331
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332
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333 #For each sample file, the following actions are done
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334 for (fileIdx in seq_len(length(fileNames(xdata)))) {
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335 #Check if the file is in the CDF format
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336 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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337
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338 # If the column isn't exist, with add one filled with NA
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339 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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340
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341 #Extract the polarity (a list of polarities)
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342 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
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343 #Verify if all the scans have the same polarity
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344 uniq_list <- unique(polarity)
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345 if (length(uniq_list) > 1) {
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346 polarity <- "mixed"
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347 } else {
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348 polarity <- as.character(uniq_list)
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349 }
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350
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351 #Set the polarity attribute
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352 sampleMetadata$polarity[fileIdx] <- polarity
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353 }
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354
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355 }
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356
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357 write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
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358
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359 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
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360
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361 }
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362
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363
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364 # This function will compute MD5 checksum to check the data integrity
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365 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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366 getMd5sum <- function(files) {
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367 cat("Compute md5 checksum...\n")
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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368 library(tools)
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369 return(as.matrix(md5sum(files)))
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370 }
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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371
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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372 # This function retrieve the raw file in the working directory
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373 # - if zipfile: unzip the file with its directory tree
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374 # - if singlefiles: set symlink with the good filename
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375 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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376 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
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377
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378 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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379
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380 # single - if the file are passed in the command arguments -> refresh singlefile
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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381 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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382 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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383 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
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384
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385 singlefile <- NULL
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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386 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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387 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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388 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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389 # In case, an url is used to import data within Galaxy
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390 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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391 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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392 }
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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393 }
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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394 # zipfile - if the file are passed in the command arguments -> refresh zipfile
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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395 if (!is.null(args[[paste0("zipfile", prefix)]]))
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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396 zipfile <- args[[paste0("zipfile", prefix)]]
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397
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398 # single
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399 if (!is.null(singlefile) && (length("singlefile") > 0)) {
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400 files <- vector()
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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401 for (singlefile_sampleName in names(singlefile)) {
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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402 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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403 if (!file.exists(singlefile_galaxyPath)) {
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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404 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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405 print(error_message)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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406 stop(error_message)
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407 }
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408
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409 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE)))
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410 file.copy(singlefile_galaxyPath, singlefile_sampleName)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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411 files <- c(files, singlefile_sampleName)
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412 }
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413 }
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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414 # zipfile
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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415 if (!is.null(zipfile) && (zipfile != "")) {
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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416 if (!file.exists(zipfile)) {
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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417 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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418 print(error_message)
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419 stop(error_message)
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420 }
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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421 suppressWarnings(unzip(zipfile, unzip = "unzip"))
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422
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423 #get the directory name
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424 suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))
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425 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
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426 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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427 directory <- "."
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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428 if (length(directories) == 1) directory <- directories
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429
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430 cat("files_root_directory\t", directory, "\n")
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431
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432 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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433 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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434 info <- file.info(directory)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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435 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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436 files <- c(directory[!info$isdir], listed)
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437 exists <- file.exists(files)
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438 files <- files[exists]
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439
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440 }
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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441 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
4
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442 }
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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443
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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444
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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445 # This function retrieve a xset like object
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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446 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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447 getxcmsSetObject <- function(xobject) {
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2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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448 # XCMS 1.x
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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449 if (class(xobject) == "xcmsSet")
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
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450 return(xobject)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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451 # XCMS 3.x
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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452 if (class(xobject) == "XCMSnExp") {
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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453 # Get the legacy xcmsSet object
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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454 suppressWarnings(xset <- as(xobject, "xcmsSet"))
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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455 if (!is.null(xset@phenoData$sample_group))
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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456 sampclass(xset) <- xset@phenoData$sample_group
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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457 else
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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458 sampclass(xset) <- "."
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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459 return(xset)
2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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460 }
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833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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461 }