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annotate lib.r @ 32:68282292acc4 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:39:07 -0400
parents f248fd3b89d6
children 59943e24684b
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
1 #@authors ABiMS TEAM, Y. Guitton
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
4 #@author G. Le Corguille
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
6 parseCommandArgs <- function(...) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
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7 args <- batch::parseCommandArgs(...)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
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8 for (key in names(args)) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
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9 if (args[key] %in% c("TRUE","FALSE"))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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10 args[key] = as.logical(args[key])
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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11 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
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12 return(args)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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13 }
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fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
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15 #@author G. Le Corguille
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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16 # This function will
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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17 # - load the packages
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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18 # - display the sessionInfo
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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19 loadAndDisplayPackages <- function(pkgs) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
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22 sessioninfo = sessionInfo()
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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23 cat(sessioninfo$R.version$version.string,"\n")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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24 cat("Main packages:\n")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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26 cat("Other loaded packages:\n")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
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28 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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30 #@author G. Le Corguille
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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31 # This function merge several xdata into one.
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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32 mergeXData <- function(args) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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33 for(image in args$images) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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34 load(image)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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35 # Handle infiles
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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36 if (!exists("singlefile")) singlefile <- NULL
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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37 if (!exists("zipfile")) zipfile <- NULL
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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38 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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39 zipfile <- rawFilePath$zipfile
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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40 singlefile <- rawFilePath$singlefile
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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41 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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42 if (exists("raw_data")) xdata <- raw_data
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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43 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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44 cat(sampleNamesList$sampleNamesOrigin,"\n")
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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45 if (!exists("xdata_merged")) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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46 xdata_merged <- xdata
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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47 singlefile_merged <- singlefile
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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48 md5sumList_merged <- md5sumList
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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49 sampleNamesList_merged <- sampleNamesList
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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50 } else {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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51 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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52 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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53 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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54 singlefile_merged <- c(singlefile_merged,singlefile)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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55 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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56 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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57 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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58 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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59 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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60 rm(image)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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61 xdata <- xdata_merged; rm(xdata_merged)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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62 singlefile <- singlefile_merged; rm(singlefile_merged)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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63 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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64 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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66 if (!is.null(args$sampleMetadata)) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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67 cat("\tXSET PHENODATA SETTING...\n")
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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68 sampleMetadataFile <- args$sampleMetadata
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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69 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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70 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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72 if (any(is.na(pData(xdata)$sample_group))) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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73 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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74 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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75 print(error_message)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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76 stop(error_message)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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77 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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78 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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79 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList))
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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80 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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81
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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82 #@author G. Le Corguille
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83 # This function convert if it is required the Retention Time in minutes
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84 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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85 if (convertRTMinute){
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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86 #converting the retention times (seconds) into minutes
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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87 print("converting the retention times into minutes in the variableMetadata")
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88 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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89 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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90 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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91 }
206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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92 return (variableMetadata)
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93 }
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94
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95 #@author G. Le Corguille
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96 # This function format ions identifiers
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97 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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98 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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99 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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100 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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101 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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102 return(variableMetadata)
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103 }
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104
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105 #@author G. Le Corguille
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106 # Draw the plotChromPeakDensity 3 per page in a pdf file
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107 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
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108 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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109
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110 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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111
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112 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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113 names(group_colors) <- unique(xdata$sample_group)
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114
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115 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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116 for (i in 1:nrow(featureDefinitions(xdata))) {
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117 mzmin = featureDefinitions(xdata)[i,]$mzmin
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118 mzmax = featureDefinitions(xdata)[i,]$mzmax
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119 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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120 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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121 }
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122
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123 dev.off()
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124 }
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125
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126 #@author G. Le Corguille
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127 # Draw the plotChromPeakDensity 3 per page in a pdf file
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128 getPlotAdjustedRtime <- function(xdata) {
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129
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130 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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131
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132 # Color by group
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133 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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134 if (length(group_colors) > 1) {
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135 names(group_colors) <- unique(xdata$sample_group)
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136 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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137 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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138 }
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139
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140 # Color by sample
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141 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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142 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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143
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144 dev.off()
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145 }
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146
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147 #@author G. Le Corguille
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148 # value: intensity values to be used into, maxo or intb
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149 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
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150 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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151 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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152 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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153 variableMetadata <- featureDefinitions(xdata)
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154 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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155 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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156
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157 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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158 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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159
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160 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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161 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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162
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163 }
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164
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165 #@author G. Le Corguille
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166 # It allow different of field separators
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167 getDataFrameFromFile <- function(filename, header=T) {
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168 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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169 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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170 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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171 if (ncol(myDataFrame) < 2) {
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172 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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173 print(error_message)
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174 stop(error_message)
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175 }
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176 return(myDataFrame)
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177 }
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178
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179 getPlotChromatogram <- function(xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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180
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181 chrom <- chromatogram(xdata, aggregationFun = aggregationFun)
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182 if (aggregationFun == "sum")
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183 type="Total Ion Chromatograms"
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184 else
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185 type="Base Peak Intensity Chromatograms"
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186
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187 adjusted="Raw"
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188 if (hasAdjustedRtime(xdata))
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189 adjusted="Adjusted"
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190
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191 main <- paste(type,":",adjusted,"data")
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192
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193 pdf(pdfname, width=16, height=10)
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194
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195 # Color by group
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196 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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197 if (length(group_colors) > 1) {
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198 names(group_colors) <- unique(xdata$sample_group)
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199 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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200 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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201 }
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202
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203 # Color by sample
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204 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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205 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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206
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207 dev.off()
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208 }
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209
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210 #@author G. Le Corguille
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211 getPlotTICs <- function(xdata, pdfname="TICs.pdf") {
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212 getPlotChromatogram(xdata, pdfname, aggregationFun = "sum")
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213 }
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214
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215 #@author G. Le Corguille
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216 getPlotBPIs <- function(xdata, pdfname="BPIs.pdf") {
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217 getPlotChromatogram(xdata, pdfname, aggregationFun = "max")
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218 }
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219
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220
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221 # Get the polarities from all the samples of a condition
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222 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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223 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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224 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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225 cat("Creating the sampleMetadata file...\n")
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226
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227 #Create the sampleMetada dataframe
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228 sampleMetadata <- xdata@phenoData@data
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229 rownames(sampleMetadata) <- NULL
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230 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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231
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232 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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233 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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234
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235 if (any(duplicated(sampleNamesMakeNames))) {
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236 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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237 for (sampleName in sampleNamesOrigin) {
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238 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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239 }
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240 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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241 }
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242
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243 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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244 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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245 for (sampleName in sampleNamesOrigin) {
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246 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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247 }
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248 }
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249
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250 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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251
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252
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253 #For each sample file, the following actions are done
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254 for (fileIdx in 1:length(fileNames(xdata))) {
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255 #Check if the file is in the CDF format
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256 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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257
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258 # If the column isn't exist, with add one filled with NA
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259 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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260
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261 #Extract the polarity (a list of polarities)
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262 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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263 #Verify if all the scans have the same polarity
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264 uniq_list <- unique(polarity)
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265 if (length(uniq_list)>1){
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266 polarity <- "mixed"
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267 } else {
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268 polarity <- as.character(uniq_list)
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269 }
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270
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271 #Set the polarity attribute
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272 sampleMetadata$polarity[fileIdx] <- polarity
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273 }
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275 }
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277 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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278
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279 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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280
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281 }
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283
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284 # This function check if xcms will found all the files
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285 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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286 checkFilesCompatibilityWithXcms <- function(directory) {
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287 cat("Checking files filenames compatibilities with xmcs...\n")
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288 # WHAT XCMS WILL FIND
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289 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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290 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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291 info <- file.info(directory)
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292 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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293 files <- c(directory[!info$isdir], listed)
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294 files_abs <- file.path(getwd(), files)
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295 exists <- file.exists(files_abs)
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296 files[exists] <- files_abs[exists]
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297 files[exists] <- sub("//","/",files[exists])
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298
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299 # WHAT IS ON THE FILESYSTEM
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300 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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301 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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302
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303 # COMPARISON
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304 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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305 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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306 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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307 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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308 }
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309 }
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310
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311
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312 #This function list the compatible files within the directory as xcms did
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313 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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314 getMSFiles <- function (directory) {
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315 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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316 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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317 info <- file.info(directory)
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318 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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319 files <- c(directory[!info$isdir], listed)
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320 exists <- file.exists(files)
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321 files <- files[exists]
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322 return(files)
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323 }
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324
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325 # This function check if XML contains special caracters. It also checks integrity and completness.
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326 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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327 checkXmlStructure <- function (directory) {
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328 cat("Checking XML structure...\n")
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329
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330 cmd <- paste0("IFS=$'\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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331 capture <- system(cmd, intern=TRUE)
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332
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333 if (length(capture)>0){
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334 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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335 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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336 write(capture, stderr())
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337 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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338 }
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339
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340 }
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341
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342
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343 # This function check if XML contain special characters
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344 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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345 deleteXmlBadCharacters<- function (directory) {
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346 cat("Checking Non ASCII characters in the XML...\n")
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347
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348 processed <- F
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349 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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350 for (i in l){
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351 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
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352 capture <- suppressWarnings(system(cmd, intern=TRUE))
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353 if (length(capture)>0){
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354 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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355 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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356 c <- system(cmd, intern=TRUE)
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357 capture <- ""
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358 processed <- T
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359 }
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360 }
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361 if (processed) cat("\n\n")
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362 return(processed)
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363 }
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364
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365
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366 # This function will compute MD5 checksum to check the data integrity
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367 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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368 getMd5sum <- function (directory) {
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369 cat("Compute md5 checksum...\n")
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370 # WHAT XCMS WILL FIND
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371 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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372 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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373 info <- file.info(directory)
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374 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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375 files <- c(directory[!info$isdir], listed)
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376 exists <- file.exists(files)
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377 files <- files[exists]
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378
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diff changeset
379 library(tools)
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diff changeset
380
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f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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381 #cat("\n\n")
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382
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diff changeset
383 return(as.matrix(md5sum(files)))
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diff changeset
384 }
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lecorguille
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diff changeset
385
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lecorguille
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386
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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387 # This function get the raw file path from the arguments
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388 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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389 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
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lecorguille
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390 if (!is.null(args$zipfile)) zipfile <- args$zipfile
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lecorguille
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diff changeset
391 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
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392 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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393
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lecorguille
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394 if (!is.null(args$singlefile_galaxyPath)) {
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lecorguille
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395 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
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396 singlefile_sampleNames <- args$singlefile_sampleName
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lecorguille
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397 }
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lecorguille
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398 if (!is.null(args$singlefile_galaxyPathPositive)) {
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lecorguille
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399 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
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400 singlefile_sampleNames <- args$singlefile_sampleNamePositive
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lecorguille
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401 }
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lecorguille
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diff changeset
402 if (!is.null(args$singlefile_galaxyPathNegative)) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
403 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
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lecorguille
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404 singlefile_sampleNames <- args$singlefile_sampleNameNegative
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lecorguille
parents: 17
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405 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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406 if (exists("singlefile_galaxyPaths")){
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cc3a32791781 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
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407 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
cc3a32791781 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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408 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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409
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lecorguille
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410 singlefile <- NULL
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
411 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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412 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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413 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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414 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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lecorguille
parents: 17
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415 }
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lecorguille
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416 }
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68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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417 return(list(zipfile=zipfile, singlefile=singlefile))
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lecorguille
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418 }
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lecorguille
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419
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lecorguille
parents: 17
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420
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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421 # This function retrieve the raw file in the working directory
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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422 # - if zipfile: unzip the file with its directory tree
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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423 # - if singlefiles: set symlink with the good filename
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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424 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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lecorguille
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425 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
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426 if(!is.null(singlefile) && (length("singlefile")>0)) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
427 for (singlefile_sampleName in names(singlefile)) {
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diff changeset
428 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
429 if(!file.exists(singlefile_galaxyPath)){
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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430 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
431 print(error_message); stop(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
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432 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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433
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434 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
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lecorguille
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diff changeset
435 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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lecorguille
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436
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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437 }
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438 directory <- "."
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lecorguille
parents: 17
diff changeset
439
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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440 }
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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441 if(!is.null(zipfile) && (zipfile != "")) {
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
442 if(!file.exists(zipfile)){
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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443 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
444 print(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
445 stop(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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446 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
447
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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448 #list all file in the zip file
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lecorguille
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449 #zip_files <- unzip(zipfile,list=T)[,"Name"]
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lecorguille
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diff changeset
450
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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451 #unzip
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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452 suppressWarnings(unzip(zipfile, unzip="unzip"))
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
453
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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454 #get the directory name
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
455 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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456 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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457 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
458 directory <- "."
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
459 if (length(directories) == 1) directory <- directories
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
460
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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461 cat("files_root_directory\t",directory,"\n")
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
462
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
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463 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
464 return (directory)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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465 }
29
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lecorguille
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diff changeset
466
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lecorguille
parents: 28
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467
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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468 # This function retrieve a xset like object
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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469 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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470 getxcmsSetObject <- function(xobject) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
471 # XCMS 1.x
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diff changeset
472 if (class(xobject) == "xcmsSet")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
473 return (xobject)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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474 # XCMS 3.x
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475 if (class(xobject) == "XCMSnExp") {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
476 # Get the legacy xcmsSet object
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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477 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
478 sampclass(xset) <- xset@phenoData$sample_group
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
479 return (xset)
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480 }
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lecorguille
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diff changeset
481 }
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diff changeset
482
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
483
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
484 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
485 # https://github.com/sneumann/xcms/issues/250
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
486 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
487 mzfmt <- paste("%.", mzdec, "f", sep = "")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
488 rtfmt <- paste("%.", rtdec, "f", sep = "")
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lecorguille
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diff changeset
489
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
490 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
491 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
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lecorguille
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diff changeset
492
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diff changeset
493 if (any(dup <- duplicated(gnames)))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
494 for (dupname in unique(gnames[dup])) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
495 dupidx <- which(gnames == dupname)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
496 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
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lecorguille
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497 }
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lecorguille
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diff changeset
498
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
499 return (gnames)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
500 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
501
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
502 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
503 # https://github.com/sneumann/xcms/issues/247
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
504 .concatenate_XCMSnExp <- function(...) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
505 x <- list(...)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
506 if (length(x) == 0)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
507 return(NULL)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
508 if (length(x) == 1)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
509 return(x[[1]])
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
510 ## Check that all are XCMSnExp objects.
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
511 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
512 stop("All passed objects should be 'XCMSnExp' objects")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
513 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
514 ## If any of the XCMSnExp has alignment results or detected features drop
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
515 ## them!
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
516 x <- lapply(x, function(z) {
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lecorguille
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diff changeset
517 if (hasAdjustedRtime(z)) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
518 z <- dropAdjustedRtime(z)
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lecorguille
parents: 28
diff changeset
519 warning("Adjusted retention times found, had to drop them.")
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lecorguille
parents: 28
diff changeset
520 }
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lecorguille
parents: 28
diff changeset
521 if (hasFeatures(z)) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
522 z <- dropFeatureDefinitions(z)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
523 warning("Feature definitions found, had to drop them.")
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lecorguille
parents: 28
diff changeset
524 }
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lecorguille
parents: 28
diff changeset
525 z
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lecorguille
parents: 28
diff changeset
526 })
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lecorguille
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diff changeset
527 ## Combine peaks
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
528 fls <- lapply(x, fileNames)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
529 startidx <- cumsum(lengths(fls))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
530 pks <- lapply(x, chromPeaks)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
531 procH <- lapply(x, processHistory)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
532 for (i in 2:length(fls)) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
533 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
534 procH[[i]] <- lapply(procH[[i]], function(z) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
535 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
536 z
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lecorguille
parents: 28
diff changeset
537 })
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
538 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
539 pks <- do.call(rbind, pks)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
540 new_x@.processHistory <- unlist(procH)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
541 chromPeaks(new_x) <- pks
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
542 if (validObject(new_x))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
543 new_x
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lecorguille
parents: 28
diff changeset
544 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
545
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
546 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
547 # https://github.com/sneumann/xcms/issues/247
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
548 .concatenate_OnDiskMSnExp <- function(...) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
549 x <- list(...)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
550 if (length(x) == 0)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
551 return(NULL)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
552 if (length(x) == 1)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
553 return(x[[1]])
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
554 ## Check that all are XCMSnExp objects.
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
555 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents: 28
diff changeset
556 stop("All passed objects should be 'OnDiskMSnExp' objects")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
557 ## Check processingQueue
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
558 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
559 new_procQ <- procQ[[1]]
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
560 is_ok <- unlist(lapply(procQ, function(z)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
561 !is.character(all.equal(new_procQ, z))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
562 ))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
563 if (any(!is_ok)) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
564 warning("Processing queues from the submitted objects differ! ",
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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565 "Dropping the processing queue.")
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566 new_procQ <- list()
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567 }
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568 ## processingData
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569 fls <- lapply(x, function(z) z@processingData@files)
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570 startidx <- cumsum(lengths(fls))
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571 ## featureData
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572 featd <- lapply(x, fData)
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573 ## Have to update the file index and the spectrum names.
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574 for (i in 2:length(featd)) {
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575 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
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576 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
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577 fileIds = featd[[i]]$fileIdx,
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578 spectrumIds = featd[[i]]$spIdx,
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579 nSpectra = nrow(featd[[i]]),
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580 nFiles = length(unlist(fls))
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lecorguille
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581 )
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582 }
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lecorguille
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583 featd <- do.call(rbind, featd)
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lecorguille
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584 featd$spectrum <- 1:nrow(featd)
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585 ## experimentData
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586 expdata <- lapply(x, function(z) {
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587 ed <- z@experimentData
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588 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
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589 instrumentModel = ed@instrumentModel,
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590 ionSource = ed@ionSource,
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591 analyser = ed@analyser,
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592 detectorType = ed@detectorType,
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593 stringsAsFactors = FALSE)
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594 })
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595 expdata <- do.call(rbind, expdata)
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596 expdata <- new("MIAPE",
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597 instrumentManufacturer = expdata$instrumentManufacturer,
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598 instrumentModel = expdata$instrumentModel,
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599 ionSource = expdata$ionSource,
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600 analyser = expdata$analyser,
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601 detectorType = expdata$detectorType)
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602
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603 ## protocolData
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604 protodata <- lapply(x, function(z) z@protocolData)
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605 if (any(unlist(lapply(protodata, nrow)) > 0))
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606 warning("Found non-empty protocol data, but merging protocol data is",
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607 " currently not supported. Skipped.")
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608 ## phenoData
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609 pdata <- do.call(rbind, lapply(x, pData))
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610 res <- new(
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611 "OnDiskMSnExp",
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612 phenoData = new("NAnnotatedDataFrame", data = pdata),
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613 featureData = new("AnnotatedDataFrame", featd),
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614 processingData = new("MSnProcess",
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615 processing = paste0("Concatenated [", date(), "]"),
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616 files = unlist(fls), smoothed = NA),
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617 experimentData = expdata,
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618 spectraProcessingQueue = new_procQ)
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619 if (validObject(res))
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620 res
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621 }
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622
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623 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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624 # https://github.com/sneumann/xcms/issues/247
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625 c.XCMSnExp <- function(...) {
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626 .concatenate_XCMSnExp(...)
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627 }
32
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628
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629 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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630 # https://github.com/sneumann/xcms/issues/247
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631 c.MSnbase <- function(...) {
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632 .concatenate_OnDiskMSnExp(...)
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633 }