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annotate lib.r @ 45:43122259be1f draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 15:56:21 +0000
parents 9df658383852
children 18d050f7b9d4
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3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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1 #@authors ABiMS TEAM, Y. Guitton
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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4 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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6 parseCommandArgs <- function(...) {
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43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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7 args <- batch::parseCommandArgs(...)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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8 for (key in names(args)) {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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9 if (args[key] %in% c("TRUE", "FALSE"))
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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10 args[key] <- as.logical(args[key])
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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11 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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12 return(args)
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3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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13 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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15 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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16 # This function will
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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17 # - load the packages
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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18 # - display the sessionInfo
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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19 loadAndDisplayPackages <- function(pkgs) {
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43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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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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3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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22 sessioninfo <- sessionInfo()
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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23 cat(sessioninfo$R.version$version.string, "\n")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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24 cat("Main packages:\n")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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25 for (pkg in names(sessioninfo$otherPkgs)) {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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26 cat(paste(pkg, packageVersion(pkg)), "\t")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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27 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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28 cat("\n")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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29 cat("Other loaded packages:\n")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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30 for (pkg in names(sessioninfo$loadedOnly)) {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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31 cat(paste(pkg, packageVersion(pkg)), "\t")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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32 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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33 cat("\n")
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3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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34 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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36 #@author G. Le Corguille
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e64491a96c95 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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37 # This function merge several chromBPI or chromTIC into one.
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79fe34cedc56 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
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38 mergeChrom <- function(chrom_merged, chrom) {
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43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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39 if (is.null(chrom_merged)) return(NULL)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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40 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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41 return(chrom_merged)
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42 }
e64491a96c95 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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e64491a96c95 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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44 #@author G. Le Corguille
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de3b88417327 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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45 # This function merge several xdata into one.
de3b88417327 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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46 mergeXData <- function(args) {
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43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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47 chromTIC <- NULL
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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48 chromBPI <- NULL
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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49 chromTIC_adjusted <- NULL
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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50 chromBPI_adjusted <- NULL
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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51 md5sumList <- NULL
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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52 for (image in args$images) {
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54 load(image)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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55 # Handle infiles
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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56 if (!exists("singlefile")) singlefile <- NULL
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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57 if (!exists("zipfile")) zipfile <- NULL
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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59 zipfile <- rawFilePath$zipfile
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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60 singlefile <- rawFilePath$singlefile
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62 if (exists("raw_data")) xdata <- raw_data
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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63 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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65 cat(sampleNamesList$sampleNamesOrigin, "\n")
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66
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67 if (!exists("xdata_merged")) {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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68 xdata_merged <- xdata
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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69 singlefile_merged <- singlefile
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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70 md5sumList_merged <- md5sumList
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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71 sampleNamesList_merged <- sampleNamesList
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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72 chromTIC_merged <- chromTIC
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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73 chromBPI_merged <- chromBPI
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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74 chromTIC_adjusted_merged <- chromTIC_adjusted
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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75 chromBPI_adjusted_merged <- chromBPI_adjusted
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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76 } else {
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77 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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78 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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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)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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82 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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83 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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84 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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85 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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86 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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87 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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88 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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89 }
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90 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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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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9df658383852 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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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$sample_name)), cex = 0.8, lty = 1)
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296
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297 dev.off()
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298 }
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299
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300
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301 # Get the polarities from all the samples of a condition
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302 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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303 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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9df658383852 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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304 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
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305 cat("Creating the sampleMetadata file...\n")
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306
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307 #Create the sampleMetada dataframe
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308 sampleMetadata <- xdata@phenoData@data
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309 rownames(sampleMetadata) <- NULL
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310 colnames(sampleMetadata) <- c("sample_name", "class")
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311
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312 sampleNamesOrigin <- sampleMetadata$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")
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368 library(tools)
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369 return(as.matrix(md5sum(files)))
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370 }
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371
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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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9df658383852 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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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
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381 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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382 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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383 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
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384
45
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385 singlefile <- NULL
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386 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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387 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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388 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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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)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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391 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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392 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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393 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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394 # zipfile - if the file are passed in the command arguments -> refresh zipfile
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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395 if (!is.null(args[[paste0("zipfile", prefix)]]))
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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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()
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401 for (singlefile_sampleName in names(singlefile)) {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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402 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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403 if (!file.exists(singlefile_galaxyPath)) {
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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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!")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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405 print(error_message)
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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)
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411 files <- c(files, singlefile_sampleName)
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412 }
45
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413 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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414 # zipfile
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415 if (!is.null(zipfile) && (zipfile != "")) {
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416 if (!file.exists(zipfile)) {
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417 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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418 print(error_message)
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419 stop(error_message)
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420 }
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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421 suppressWarnings(unzip(zipfile, unzip = "unzip"))
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422
45
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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)$isdir]
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427 directory <- "."
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428 if (length(directories) == 1) directory <- directories
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429
45
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430 cat("files_root_directory\t", directory, "\n")
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431
45
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432 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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433 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
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434 info <- file.info(directory)
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435 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
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436 files <- c(directory[!info$isdir], listed)
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437 exists <- file.exists(files)
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438 files <- files[exists]
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439
45
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440 }
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441 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
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442 }
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443
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444
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445 # This function retrieve a xset like object
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446 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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447 getxcmsSetObject <- function(xobject) {
45
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448 # XCMS 1.x
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449 if (class(xobject) == "xcmsSet")
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450 return(xobject)
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451 # XCMS 3.x
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452 if (class(xobject) == "XCMSnExp") {
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453 # Get the legacy xcmsSet object
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454 suppressWarnings(xset <- as(xobject, "xcmsSet"))
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455 if (!is.null(xset@phenoData$sample_group))
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parents: 44
diff changeset
456 sampclass(xset) <- xset@phenoData$sample_group
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 44
diff changeset
457 else
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 44
diff changeset
458 sampclass(xset) <- "."
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 44
diff changeset
459 return(xset)
43122259be1f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 44
diff changeset
460 }
29
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff changeset
461 }