Mercurial > repos > lecorguille > xcms_merge

annotate xcms_merge.r @ 9:35b9bb3205d8 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1444e7c7ebd2bb5bdadede71c60a39f560721a98
author lecorguille
date Mon, 05 Mar 2018 09:31:22 -0500
parents 6b5504f877ff
children 47e953d9da82
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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1 #!/usr/bin/env Rscript
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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3 #Import the different functions
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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4 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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5 source_local("lib.r")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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7 pkgs <- c("xcms","batch")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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8 loadAndDisplayPackages(pkgs)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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9 cat("\n\n");
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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11 args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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14 cat("\tXSET MERGING...\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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16 for(image in args$images) {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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17 load(image)
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lecorguille
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19 # Handle infiles
35b9bb3205d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1444e7c7ebd2bb5bdadede71c60a39f560721a98
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20 if (!exists("singlefile")) singlefile <- NULL
35b9bb3205d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1444e7c7ebd2bb5bdadede71c60a39f560721a98
lecorguille
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21 if (!exists("zipfile")) zipfile <- NULL
35b9bb3205d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1444e7c7ebd2bb5bdadede71c60a39f560721a98
lecorguille
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22 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
35b9bb3205d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1444e7c7ebd2bb5bdadede71c60a39f560721a98
lecorguille
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23 zipfile <- rawFilePath$zipfile
35b9bb3205d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1444e7c7ebd2bb5bdadede71c60a39f560721a98
lecorguille
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24 singlefile <- rawFilePath$singlefile
35b9bb3205d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1444e7c7ebd2bb5bdadede71c60a39f560721a98
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25 args <- rawFilePath$args
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26 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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27
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28 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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29 cat(sampleNamesList$sampleNamesOrigin,"\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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30 if (!exists("xdata_merged")) {
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31 xdata_merged <- xdata
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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32 singlefile_merged <- singlefile
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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33 md5sumList_merged <- md5sumList
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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34 sampleNamesList_merged <- sampleNamesList
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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35 } else {
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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36 xdata_merged <- c(xdata_merged,xdata)
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37 singlefile_merged <- c(singlefile_merged,singlefile)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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38 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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39 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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40 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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41 }
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42 }
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43 rm(image)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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44 xdata <- xdata_merged; rm(xdata_merged)
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45 singlefile <- singlefile_merged; rm(singlefile_merged)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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46 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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47 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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49 if (!is.null(args$sampleMetadata)) {
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50 cat("\tXSET PHENODATA SETTING...\n")
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51 sampleMetadataFile <- args$sampleMetadata
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52 sampleMetadata <- read.table(sampleMetadataFile, h=F, sep=";", stringsAsFactors=F)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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53 if (ncol(sampleMetadata) < 2) sampleMetadata <- read.table(sampleMetadataFile, h=F, sep="\t", stringsAsFactors=F)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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54 if (ncol(sampleMetadata) < 2) sampleMetadata <- read.table(sampleMetadataFile, h=F, sep=",", stringsAsFactors=F)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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55 if (ncol(sampleMetadata) < 2) {
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56 error_message="Your sampleMetadata file seems not well formatted. The column separators accepted are ; , and tabulation"
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57 print(error_message)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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58 stop(error_message)
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59 }
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60 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
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62 if (any(is.na(pData(xdata)$sample_group))) {
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63 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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64 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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65 print(error_message)
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66 stop(error_message)
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67 }
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68 }
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70 # Create a sampleMetada file
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71 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")
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73 # Get the legacy xcmsSet object
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74 xset <- getxcmsSetObject(xdata)
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76 cat("\n\n")
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79 # -- TIC --
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80 cat("\t\tGET TIC GRAPH\n")
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81 #@TODO: one day, use xdata instead of xset to draw the TICs and BPC or a complete other method
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82 getTICs(xcmsSet=xset, rt="raw", pdfname="TICs.pdf")
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83 getBPCs(xcmsSet=xset, rt="raw", pdfname="BICs.pdf")
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84
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85 cat("\n\n")
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87 cat("\tXCMSnExp OBJECT INFO\n")
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88 print(pData(xdata))
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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89 print(xdata)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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90 cat("\n\n")
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92 cat("\txcmsSet OBJECT INFO\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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93 # Get the legacy xcmsSet object
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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94 xset <- getxcmsSetObject(xdata)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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95 print(xset@phenoData)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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96 print(xset)
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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97 cat("\n\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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98
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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99 cat("\tSAVE RData\n")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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100 #saving R data in .Rdata file to save the variables used in the present tool
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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101 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
dca722aecb67 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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102 save(list=objects2save[objects2save %in% ls()], file="merged.RData")