Mercurial > repos > lecorguille > xcms_xcmsset

annotate lib.r @ 22:1f6fb923bc4a draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
author lecorguille
date Thu, 07 Mar 2019 07:36:19 -0500
parents 87df3692c68d
children 5c62dfdb64f4
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
1 #@authors ABiMS TEAM, Y. Guitton
b62808a2a008 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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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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4 #@author G. Le Corguille
b62808a2a008 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
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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6 parseCommandArgs <- function(...) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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7 args <- batch::parseCommandArgs(...)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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8 for (key in names(args)) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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9 if (args[key] %in% c("TRUE","FALSE"))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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10 args[key] = as.logical(args[key])
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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11 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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12 return(args)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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13 }
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0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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15 #@author G. Le Corguille
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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16 # This function will
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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17 # - load the packages
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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18 # - display the sessionInfo
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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19 loadAndDisplayPackages <- function(pkgs) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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22 sessioninfo = sessionInfo()
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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23 cat(sessioninfo$R.version$version.string,"\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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24 cat("Main packages:\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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26 cat("Other loaded packages:\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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28 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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30 #@author G. Le Corguille
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lecorguille
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31 # This function merge several chromBPI or chromTIC into one.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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32 mergeChrom <- function(chrom_merged, chrom) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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33 if (is.null(chrom_merged)) return(NULL)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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35 return(chrom_merged)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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36 }
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38 #@author G. Le Corguille
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39 # This function merge several xdata into one.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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40 mergeXData <- function(args) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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41 chromTIC <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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42 chromBPI <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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43 chromTIC_adjusted <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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44 chromBPI_adjusted <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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45 for(image in args$images) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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47 load(image)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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48 # Handle infiles
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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49 if (!exists("singlefile")) singlefile <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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50 if (!exists("zipfile")) zipfile <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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52 zipfile <- rawFilePath$zipfile
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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53 singlefile <- rawFilePath$singlefile
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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55
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56 if (exists("raw_data")) xdata <- raw_data
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lecorguille
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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58
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59 cat(sampleNamesList$sampleNamesOrigin,"\n")
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60
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lecorguille
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61 if (!exists("xdata_merged")) {
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lecorguille
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62 xdata_merged <- xdata
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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63 singlefile_merged <- singlefile
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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64 md5sumList_merged <- md5sumList
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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65 sampleNamesList_merged <- sampleNamesList
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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66 chromTIC_merged <- chromTIC
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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67 chromBPI_merged <- chromBPI
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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68 chromTIC_adjusted_merged <- chromTIC_adjusted
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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69 chromBPI_adjusted_merged <- chromBPI_adjusted
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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70 } else {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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74
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75 singlefile_merged <- c(singlefile_merged,singlefile)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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83 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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84 }
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85 rm(image)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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86 xdata <- xdata_merged; rm(xdata_merged)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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87 singlefile <- singlefile_merged; rm(singlefile_merged)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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 }
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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
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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 # This function convert the remain NA to 0 in the dataMatrix
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138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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139 if (naTOzero){
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140 dataMatrix[is.na(dataMatrix)] <- 0
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141 }
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142 return (dataMatrix)
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143 }
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144
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145 #@author G. Le Corguille
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146 # Draw the plotChromPeakDensity 3 per page in a pdf file
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147 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) {
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148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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149
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150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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151
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152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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153 names(group_colors) <- unique(xdata$sample_group)
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154
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155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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156 for (i in 1:nrow(featureDefinitions(xdata))) {
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157 mzmin = featureDefinitions(xdata)[i,]$mzmin
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158 mzmax = featureDefinitions(xdata)[i,]$mzmax
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159 plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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161 }
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162
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163 dev.off()
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164 }
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165
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166 #@author G. Le Corguille
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167 # Draw the plotChromPeakDensity 3 per page in a pdf file
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168 getPlotAdjustedRtime <- function(xdata) {
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169
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170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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171
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172 # Color by group
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173 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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174 if (length(group_colors) > 1) {
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175 names(group_colors) <- unique(xdata$sample_group)
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176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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178 }
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179
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180 # Color by sample
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181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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182 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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183
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184 dev.off()
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185 }
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186
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187 #@author G. Le Corguille
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188 # value: intensity values to be used into, maxo or intb
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189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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192 dataMatrix = cbind(name=groupnames(xdata), dataMatrix)
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193 variableMetadata <- featureDefinitions(xdata)
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194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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195 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata)
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196
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197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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200
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201 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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202 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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203
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204 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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205 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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206
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207 }
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208
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209 #@author G. Le Corguille
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210 # It allow different of field separators
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211 getDataFrameFromFile <- function(filename, header=T) {
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212 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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213 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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214 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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215 if (ncol(myDataFrame) < 2) {
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216 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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217 print(error_message)
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218 stop(error_message)
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219 }
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220 return(myDataFrame)
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221 }
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222
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223 #@author G. Le Corguille
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224 # Draw the BPI and TIC graphics
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225 # colored by sample names or class names
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226 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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227
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228 if (aggregationFun == "sum")
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229 type="Total Ion Chromatograms"
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230 else
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231 type="Base Peak Intensity Chromatograms"
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232
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233 adjusted="Raw"
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234 if (hasAdjustedRtime(xdata))
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235 adjusted="Adjusted"
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236
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237 main <- paste(type,":",adjusted,"data")
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238
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239 pdf(pdfname, width=16, height=10)
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240
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241 # Color by group
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242 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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243 if (length(group_colors) > 1) {
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244 names(group_colors) <- unique(xdata$sample_group)
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245 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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246 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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247 }
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248
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249 # Color by sample
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250 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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251 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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252
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253 dev.off()
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254 }
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255
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256
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257 # Get the polarities from all the samples of a condition
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258 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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259 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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260 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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261 cat("Creating the sampleMetadata file...\n")
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262
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263 #Create the sampleMetada dataframe
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264 sampleMetadata <- xdata@phenoData@data
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265 rownames(sampleMetadata) <- NULL
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266 colnames(sampleMetadata) <- c("sample_name", "class")
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267
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268 sampleNamesOrigin <- sampleMetadata$sample_name
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269 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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270
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271 if (any(duplicated(sampleNamesMakeNames))) {
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272 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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273 for (sampleName in sampleNamesOrigin) {
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274 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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275 }
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276 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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277 }
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278
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279 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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280 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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281 for (sampleName in sampleNamesOrigin) {
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282 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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283 }
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284 }
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285
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286 sampleMetadata$sample_name <- sampleNamesMakeNames
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287
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288
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289 #For each sample file, the following actions are done
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290 for (fileIdx in 1:length(fileNames(xdata))) {
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291 #Check if the file is in the CDF format
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292 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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293
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294 # If the column isn't exist, with add one filled with NA
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295 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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296
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297 #Extract the polarity (a list of polarities)
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298 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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299 #Verify if all the scans have the same polarity
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300 uniq_list <- unique(polarity)
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301 if (length(uniq_list)>1){
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302 polarity <- "mixed"
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303 } else {
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304 polarity <- as.character(uniq_list)
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305 }
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306
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307 #Set the polarity attribute
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308 sampleMetadata$polarity[fileIdx] <- polarity
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309 }
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310
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311 }
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312
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313 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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314
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315 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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316
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317 }
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318
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319
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320 # This function check if xcms will found all the files
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321 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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322 checkFilesCompatibilityWithXcms <- function(directory) {
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323 cat("Checking files filenames compatibilities with xmcs...\n")
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324 # WHAT XCMS WILL FIND
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325 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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326 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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327 info <- file.info(directory)
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328 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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329 files <- c(directory[!info$isdir], listed)
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330 files_abs <- file.path(getwd(), files)
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331 exists <- file.exists(files_abs)
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332 files[exists] <- files_abs[exists]
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333 files[exists] <- sub("//","/",files[exists])
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334
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335 # WHAT IS ON THE FILESYSTEM
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336 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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337 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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338
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339 # COMPARISON
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340 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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341 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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342 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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343 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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344 }
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345 }
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346
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347
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348 #This function list the compatible files within the directory as xcms did
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349 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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350 getMSFiles <- function (directory) {
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351 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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352 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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353 info <- file.info(directory)
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354 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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355 files <- c(directory[!info$isdir], listed)
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356 exists <- file.exists(files)
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357 files <- files[exists]
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358 return(files)
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359 }
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360
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361 # This function check if XML contains special caracters. It also checks integrity and completness.
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362 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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363 checkXmlStructure <- function (directory) {
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364 cat("Checking XML structure...\n")
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365
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366 cmd <- paste0("IFS=$'\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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367 capture <- system(cmd, intern=TRUE)
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368
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369 if (length(capture)>0){
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370 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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371 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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372 write(capture, stderr())
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373 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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374 }
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375
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376 }
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377
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378
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379 # This function check if XML contain special characters
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380 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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381 deleteXmlBadCharacters<- function (directory) {
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382 cat("Checking Non ASCII characters in the XML...\n")
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383
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384 processed <- F
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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385 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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386 for (i in l){
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387 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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388 capture <- suppressWarnings(system(cmd, intern=TRUE))
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15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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389 if (length(capture)>0){
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390 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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391 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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392 c <- system(cmd, intern=TRUE)
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393 capture <- ""
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394 processed <- T
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395 }
6
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396 }
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397 if (processed) cat("\n\n")
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398 return(processed)
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399 }
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400
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401
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402 # This function will compute MD5 checksum to check the data integrity
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403 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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404 getMd5sum <- function (directory) {
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lecorguille
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405 cat("Compute md5 checksum...\n")
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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406 # WHAT XCMS WILL FIND
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407 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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408 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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409 info <- file.info(directory)
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410 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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411 files <- c(directory[!info$isdir], listed)
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412 exists <- file.exists(files)
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413 files <- files[exists]
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414
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415 library(tools)
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diff changeset
416
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417 #cat("\n\n")
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diff changeset
418
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419 return(as.matrix(md5sum(files)))
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lecorguille
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420 }
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diff changeset
421
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lecorguille
parents: 11
diff changeset
422
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423 # This function get the raw file path from the arguments
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424 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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425 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
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426 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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lecorguille
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diff changeset
427
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428 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
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diff changeset
429
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430 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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diff changeset
431 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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diff changeset
432 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
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lecorguille
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433 }
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diff changeset
434 if (exists("singlefile_galaxyPaths")){
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
435 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
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lecorguille
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diff changeset
436 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
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lecorguille
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diff changeset
437
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438 singlefile <- NULL
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439 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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440 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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441 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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lecorguille
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diff changeset
442 # In case, an url is used to import data within Galaxy
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lecorguille
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443 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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diff changeset
444 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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445 }
15
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lecorguille
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446 }
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diff changeset
447 return(list(zipfile=zipfile, singlefile=singlefile))
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lecorguille
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diff changeset
448 }
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lecorguille
parents: 11
diff changeset
449
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
450 # This function retrieve the raw file in the working directory
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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451 # - if zipfile: unzip the file with its directory tree
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452 # - if singlefiles: set symlink with the good filename
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lecorguille
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453 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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diff changeset
454 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
455 if(!is.null(singlefile) && (length("singlefile")>0)) {
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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456 for (singlefile_sampleName in names(singlefile)) {
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lecorguille
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diff changeset
457 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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lecorguille
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diff changeset
458 if(!file.exists(singlefile_galaxyPath)){
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
459 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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460 print(error_message); stop(error_message)
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lecorguille
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461 }
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462
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463 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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464 file.copy(singlefile_galaxyPath, singlefile_sampleName)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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465
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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466 }
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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467 directory <- "."
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parents: 11
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468
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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469 }
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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470 if(!is.null(zipfile) && (zipfile != "")) {
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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471 if(!file.exists(zipfile)){
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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472 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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473 print(error_message)
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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474 stop(error_message)
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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475 }
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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476
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477 #list all file in the zip file
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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478 #zip_files <- unzip(zipfile,list=T)[,"Name"]
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479
12
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480 #unzip
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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481 suppressWarnings(unzip(zipfile, unzip="unzip"))
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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482
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483 #get the directory name
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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484 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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485 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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486 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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487 directory <- "."
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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488 if (length(directories) == 1) directory <- directories
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489
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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490 cat("files_root_directory\t",directory,"\n")
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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491
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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492 }
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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493 return (directory)
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494 }
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495
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496
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497 # This function retrieve a xset like object
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498 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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499 getxcmsSetObject <- function(xobject) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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500 # XCMS 1.x
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501 if (class(xobject) == "xcmsSet")
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502 return (xobject)
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lecorguille
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503 # XCMS 3.x
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504 if (class(xobject) == "XCMSnExp") {
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lecorguille
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505 # Get the legacy xcmsSet object
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506 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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507 if (!is.null(xset@phenoData$sample_group))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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508 sampclass(xset) <- xset@phenoData$sample_group
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509 else
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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510 sampclass(xset) <- "."
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511 return (xset)
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512 }
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513 }