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annotate lib.r @ 33:59943e24684b draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
author lecorguille
date Thu, 05 Apr 2018 18:08:20 -0400
parents 68282292acc4
children 89233250f4b0
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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
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
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4 #@author G. Le Corguille
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
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6 parseCommandArgs <- function(...) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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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
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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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206e5a968dc5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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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
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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
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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
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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
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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
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59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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31 # This function merge several chromBPI or chromTIC into one.
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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32 mergeChrom <- function(chromTIC_merged, chromTIC, xdata_merged) {
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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33 if (is.null(chromTIC_merged)) return(NULL)
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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34 chromTIC_merged@.Data <- cbind(chromTIC_merged@.Data, chromTIC@.Data)
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 32
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35 chromTIC_merged@phenoData <- xdata_merged@phenoData
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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36 return(chromTIC_merged)
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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37 }
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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39 #@author G. Le Corguille
32
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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40 # 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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41 mergeXData <- function(args) {
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59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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42 chromTIC <- NULL; chromBPI <- NULL
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68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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43 for(image in args$images) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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44 load(image)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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45 # Handle infiles
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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46 if (!exists("singlefile")) singlefile <- NULL
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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47 if (!exists("zipfile")) zipfile <- NULL
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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48 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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49 zipfile <- rawFilePath$zipfile
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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50 singlefile <- rawFilePath$singlefile
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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51 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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52 if (exists("raw_data")) xdata <- raw_data
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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53 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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54 cat(sampleNamesList$sampleNamesOrigin,"\n")
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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55 if (!exists("xdata_merged")) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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56 xdata_merged <- xdata
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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57 singlefile_merged <- singlefile
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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58 md5sumList_merged <- md5sumList
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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59 sampleNamesList_merged <- sampleNamesList
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59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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60 chromTIC_merged <- chromTIC
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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61 chromBPI_merged <- chromBPI
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lecorguille
parents: 31
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62 } else {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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63 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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64 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
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65 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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66 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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67 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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68 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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69 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
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59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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70 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC, xdata_merged)
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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71 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI, xdata_merged)
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lecorguille
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72 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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73 }
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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74 rm(image)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 31
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75 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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76 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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77 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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78 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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79 chromTIC <- chromTIC_merged; rm(chromTIC_merged)
59943e24684b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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80 chromBPI <- chromBPI_merged; rm(chromBPI_merged)
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81
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82 if (!is.null(args$sampleMetadata)) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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83 cat("\tXSET PHENODATA SETTING...\n")
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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84 sampleMetadataFile <- args$sampleMetadata
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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85 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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86 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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87
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88 if (any(is.na(pData(xdata)$sample_group))) {
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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89 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
parents: 31
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90 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
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91 print(error_message)
68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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92 stop(error_message)
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93 }
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94 }
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95 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI))
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96 }
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97
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98 #@author G. Le Corguille
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99 # This function convert if it is required the Retention Time in minutes
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100 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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101 if (convertRTMinute){
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102 #converting the retention times (seconds) into minutes
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103 print("converting the retention times into minutes in the variableMetadata")
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104 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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105 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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106 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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107 }
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108 return (variableMetadata)
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109 }
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110
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111 #@author G. Le Corguille
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112 # This function format ions identifiers
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113 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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114 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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115 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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116 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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117 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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118 return(variableMetadata)
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119 }
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120
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121 #@author G. Le Corguille
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122 # Draw the plotChromPeakDensity 3 per page in a pdf file
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123 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
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124 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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125
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126 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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127
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128 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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129 names(group_colors) <- unique(xdata$sample_group)
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130
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131 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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132 for (i in 1:nrow(featureDefinitions(xdata))) {
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133 mzmin = featureDefinitions(xdata)[i,]$mzmin
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134 mzmax = featureDefinitions(xdata)[i,]$mzmax
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135 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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136 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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137 }
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138
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139 dev.off()
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140 }
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141
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142 #@author G. Le Corguille
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143 # Draw the plotChromPeakDensity 3 per page in a pdf file
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144 getPlotAdjustedRtime <- function(xdata) {
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145
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146 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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147
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148 # Color by group
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149 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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150 if (length(group_colors) > 1) {
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151 names(group_colors) <- unique(xdata$sample_group)
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152 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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153 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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154 }
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155
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156 # Color by sample
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157 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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158 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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159
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160 dev.off()
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161 }
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162
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163 #@author G. Le Corguille
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164 # value: intensity values to be used into, maxo or intb
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165 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
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166 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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167 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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168 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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169 variableMetadata <- featureDefinitions(xdata)
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170 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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171 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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172
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173 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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174 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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175
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176 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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177 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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178
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179 }
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180
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181 #@author G. Le Corguille
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182 # It allow different of field separators
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183 getDataFrameFromFile <- function(filename, header=T) {
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184 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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185 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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186 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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187 if (ncol(myDataFrame) < 2) {
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188 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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189 print(error_message)
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190 stop(error_message)
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191 }
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192 return(myDataFrame)
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193 }
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194
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195 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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196
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197 if (aggregationFun == "sum")
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198 type="Total Ion Chromatograms"
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199 else
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200 type="Base Peak Intensity Chromatograms"
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201
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202 adjusted="Raw"
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203 if (hasAdjustedRtime(xdata))
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204 adjusted="Adjusted"
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205
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206 main <- paste(type,":",adjusted,"data")
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207
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208 pdf(pdfname, width=16, height=10)
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209
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210 # Color by group
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211 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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212 if (length(group_colors) > 1) {
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213 names(group_colors) <- unique(xdata$sample_group)
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214 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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215 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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216 }
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217
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218 # Color by sample
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219 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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220 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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221
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222 dev.off()
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223 }
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224
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225
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226 # Get the polarities from all the samples of a condition
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227 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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228 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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229 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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230 cat("Creating the sampleMetadata file...\n")
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231
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232 #Create the sampleMetada dataframe
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233 sampleMetadata <- xdata@phenoData@data
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234 rownames(sampleMetadata) <- NULL
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235 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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236
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237 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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238 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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239
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240 if (any(duplicated(sampleNamesMakeNames))) {
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241 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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242 for (sampleName in sampleNamesOrigin) {
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243 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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244 }
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245 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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246 }
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247
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248 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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249 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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250 for (sampleName in sampleNamesOrigin) {
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251 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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252 }
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253 }
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254
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255 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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256
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257
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258 #For each sample file, the following actions are done
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259 for (fileIdx in 1:length(fileNames(xdata))) {
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260 #Check if the file is in the CDF format
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261 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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262
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263 # If the column isn't exist, with add one filled with NA
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264 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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265
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266 #Extract the polarity (a list of polarities)
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267 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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268 #Verify if all the scans have the same polarity
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269 uniq_list <- unique(polarity)
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270 if (length(uniq_list)>1){
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271 polarity <- "mixed"
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272 } else {
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273 polarity <- as.character(uniq_list)
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274 }
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275
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276 #Set the polarity attribute
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277 sampleMetadata$polarity[fileIdx] <- polarity
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278 }
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279
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280 }
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281
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282 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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283
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284 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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285
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286 }
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287
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288
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289 # This function check if xcms will found all the files
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290 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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291 checkFilesCompatibilityWithXcms <- function(directory) {
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292 cat("Checking files filenames compatibilities with xmcs...\n")
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293 # WHAT XCMS WILL FIND
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294 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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295 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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296 info <- file.info(directory)
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297 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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298 files <- c(directory[!info$isdir], listed)
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299 files_abs <- file.path(getwd(), files)
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300 exists <- file.exists(files_abs)
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301 files[exists] <- files_abs[exists]
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302 files[exists] <- sub("//","/",files[exists])
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303
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304 # WHAT IS ON THE FILESYSTEM
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305 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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306 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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307
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308 # COMPARISON
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309 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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310 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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311 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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312 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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313 }
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314 }
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315
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316
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317 #This function list the compatible files within the directory as xcms did
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318 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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319 getMSFiles <- function (directory) {
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320 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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321 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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322 info <- file.info(directory)
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323 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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324 files <- c(directory[!info$isdir], listed)
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325 exists <- file.exists(files)
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326 files <- files[exists]
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327 return(files)
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328 }
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329
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330 # This function check if XML contains special caracters. It also checks integrity and completness.
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331 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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332 checkXmlStructure <- function (directory) {
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333 cat("Checking XML structure...\n")
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334
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335 cmd <- paste0("IFS=$'\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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336 capture <- system(cmd, intern=TRUE)
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337
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338 if (length(capture)>0){
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339 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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340 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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341 write(capture, stderr())
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342 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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343 }
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344
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345 }
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346
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347
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348 # This function check if XML contain special characters
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349 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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350 deleteXmlBadCharacters<- function (directory) {
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351 cat("Checking Non ASCII characters in the XML...\n")
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352
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353 processed <- F
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354 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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355 for (i in l){
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356 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
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357 capture <- suppressWarnings(system(cmd, intern=TRUE))
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358 if (length(capture)>0){
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359 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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360 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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361 c <- system(cmd, intern=TRUE)
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362 capture <- ""
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363 processed <- T
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364 }
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365 }
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366 if (processed) cat("\n\n")
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367 return(processed)
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368 }
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369
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370
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371 # This function will compute MD5 checksum to check the data integrity
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372 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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373 getMd5sum <- function (directory) {
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374 cat("Compute md5 checksum...\n")
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375 # WHAT XCMS WILL FIND
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376 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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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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377 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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378 info <- file.info(directory)
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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379 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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380 files <- c(directory[!info$isdir], listed)
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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381 exists <- file.exists(files)
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382 files <- files[exists]
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383
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f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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384 library(tools)
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385
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f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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386 #cat("\n\n")
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387
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388 return(as.matrix(md5sum(files)))
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389 }
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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390
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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391
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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392 # This function get the raw file path from the arguments
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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393 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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394 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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395 if (!is.null(args$zipfile)) zipfile <- args$zipfile
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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396 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
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lecorguille
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397 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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398
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lecorguille
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diff changeset
399 if (!is.null(args$singlefile_galaxyPath)) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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400 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
401 singlefile_sampleNames <- args$singlefile_sampleName
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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402 }
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
403 if (!is.null(args$singlefile_galaxyPathPositive)) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
404 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
405 singlefile_sampleNames <- args$singlefile_sampleNamePositive
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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406 }
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
407 if (!is.null(args$singlefile_galaxyPathNegative)) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
408 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
409 singlefile_sampleNames <- args$singlefile_sampleNameNegative
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
410 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
411 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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412 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
cc3a32791781 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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413 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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414
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diff changeset
415 singlefile <- NULL
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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416 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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diff changeset
417 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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418 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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419 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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420 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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421 }
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68282292acc4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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422 return(list(zipfile=zipfile, singlefile=singlefile))
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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423 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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424
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lecorguille
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425
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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426 # 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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427 # - if zipfile: unzip the file with its directory tree
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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428 # - 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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429 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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lecorguille
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430 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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431 if(!is.null(singlefile) && (length("singlefile")>0)) {
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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432 for (singlefile_sampleName in names(singlefile)) {
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lecorguille
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433 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
434 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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diff changeset
435 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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436 print(error_message); stop(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
437 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
438
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lecorguille
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439 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
440 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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lecorguille
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diff changeset
441
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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442 }
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diff changeset
443 directory <- "."
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
444
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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445 }
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
446 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
447 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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448 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
parents: 17
diff changeset
449 print(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
450 stop(error_message)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
451 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
452
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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453 #list all file in the zip file
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020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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454 #zip_files <- unzip(zipfile,list=T)[,"Name"]
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a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
455
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
456 #unzip
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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457 suppressWarnings(unzip(zipfile, unzip="unzip"))
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 17
diff changeset
458
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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459 #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
460 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
461 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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diff changeset
462 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
463 directory <- "."
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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464 if (length(directories) == 1) directory <- directories
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lecorguille
parents: 17
diff changeset
465
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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466 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
467
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lecorguille
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diff changeset
468 }
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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diff changeset
469 return (directory)
a79d839d625f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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470 }
29
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471
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lecorguille
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diff changeset
472
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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473 # This function retrieve a xset like object
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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474 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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475 getxcmsSetObject <- function(xobject) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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476 # XCMS 1.x
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diff changeset
477 if (class(xobject) == "xcmsSet")
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478 return (xobject)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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479 # XCMS 3.x
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480 if (class(xobject) == "XCMSnExp") {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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481 # Get the legacy xcmsSet object
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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482 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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483 sampclass(xset) <- xset@phenoData$sample_group
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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484 return (xset)
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lecorguille
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diff changeset
485 }
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lecorguille
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486 }
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lecorguille
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diff changeset
487
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lecorguille
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diff changeset
488
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
489 #@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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490 # https://github.com/sneumann/xcms/issues/250
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
491 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
492 mzfmt <- paste("%.", mzdec, "f", sep = "")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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493 rtfmt <- paste("%.", rtdec, "f", sep = "")
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lecorguille
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diff changeset
494
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495 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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496 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
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lecorguille
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diff changeset
497
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lecorguille
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498 if (any(dup <- duplicated(gnames)))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
499 for (dupname in unique(gnames[dup])) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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500 dupidx <- which(gnames == dupname)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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501 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
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lecorguille
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502 }
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lecorguille
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diff changeset
503
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
504 return (gnames)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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505 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
506
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
507 #@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
508 # https://github.com/sneumann/xcms/issues/247
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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509 .concatenate_XCMSnExp <- function(...) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
510 x <- list(...)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
511 if (length(x) == 0)
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diff changeset
512 return(NULL)
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lecorguille
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diff changeset
513 if (length(x) == 1)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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514 return(x[[1]])
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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515 ## 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
516 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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517 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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518 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
519 ## If any of the XCMSnExp has alignment results or detected features drop
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diff changeset
520 ## them!
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diff changeset
521 x <- lapply(x, function(z) {
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lecorguille
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522 if (hasAdjustedRtime(z)) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
523 z <- dropAdjustedRtime(z)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
524 warning("Adjusted retention times found, had to drop them.")
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lecorguille
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diff changeset
525 }
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lecorguille
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diff changeset
526 if (hasFeatures(z)) {
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527 z <- dropFeatureDefinitions(z)
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lecorguille
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diff changeset
528 warning("Feature definitions found, had to drop them.")
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lecorguille
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diff changeset
529 }
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lecorguille
parents: 28
diff changeset
530 z
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
531 })
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
532 ## Combine peaks
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
533 fls <- lapply(x, fileNames)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
534 startidx <- cumsum(lengths(fls))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
535 pks <- lapply(x, chromPeaks)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
536 procH <- lapply(x, processHistory)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
537 for (i in 2:length(fls)) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
538 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
539 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
540 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
541 z
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
542 })
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
543 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
544 pks <- do.call(rbind, pks)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
545 new_x@.processHistory <- unlist(procH)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
546 chromPeaks(new_x) <- pks
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
547 if (validObject(new_x))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
548 new_x
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
549 }
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
550
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
551 #@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
552 # https://github.com/sneumann/xcms/issues/247
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
553 .concatenate_OnDiskMSnExp <- function(...) {
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
554 x <- list(...)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
555 if (length(x) == 0)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
556 return(NULL)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
557 if (length(x) == 1)
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
558 return(x[[1]])
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
559 ## Check that all are XCMSnExp objects.
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 28
diff changeset
560 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
561 stop("All passed objects should be 'OnDiskMSnExp' objects")
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562 ## Check processingQueue
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563 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
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564 new_procQ <- procQ[[1]]
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565 is_ok <- unlist(lapply(procQ, function(z)
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566 !is.character(all.equal(new_procQ, z))
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567 ))
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568 if (any(!is_ok)) {
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569 warning("Processing queues from the submitted objects differ! ",
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570 "Dropping the processing queue.")
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571 new_procQ <- list()
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572 }
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573 ## processingData
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574 fls <- lapply(x, function(z) z@processingData@files)
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575 startidx <- cumsum(lengths(fls))
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576 ## featureData
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577 featd <- lapply(x, fData)
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578 ## Have to update the file index and the spectrum names.
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579 for (i in 2:length(featd)) {
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580 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
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581 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
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582 fileIds = featd[[i]]$fileIdx,
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583 spectrumIds = featd[[i]]$spIdx,
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584 nSpectra = nrow(featd[[i]]),
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585 nFiles = length(unlist(fls))
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586 )
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587 }
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588 featd <- do.call(rbind, featd)
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589 featd$spectrum <- 1:nrow(featd)
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590 ## experimentData
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591 expdata <- lapply(x, function(z) {
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592 ed <- z@experimentData
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593 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
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594 instrumentModel = ed@instrumentModel,
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595 ionSource = ed@ionSource,
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596 analyser = ed@analyser,
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597 detectorType = ed@detectorType,
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598 stringsAsFactors = FALSE)
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599 })
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600 expdata <- do.call(rbind, expdata)
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601 expdata <- new("MIAPE",
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602 instrumentManufacturer = expdata$instrumentManufacturer,
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603 instrumentModel = expdata$instrumentModel,
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604 ionSource = expdata$ionSource,
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605 analyser = expdata$analyser,
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606 detectorType = expdata$detectorType)
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607
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608 ## protocolData
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609 protodata <- lapply(x, function(z) z@protocolData)
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610 if (any(unlist(lapply(protodata, nrow)) > 0))
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611 warning("Found non-empty protocol data, but merging protocol data is",
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612 " currently not supported. Skipped.")
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613 ## phenoData
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614 pdata <- do.call(rbind, lapply(x, pData))
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615 res <- new(
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616 "OnDiskMSnExp",
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617 phenoData = new("NAnnotatedDataFrame", data = pdata),
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618 featureData = new("AnnotatedDataFrame", featd),
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619 processingData = new("MSnProcess",
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620 processing = paste0("Concatenated [", date(), "]"),
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621 files = unlist(fls), smoothed = NA),
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622 experimentData = expdata,
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623 spectraProcessingQueue = new_procQ)
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624 if (validObject(res))
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625 res
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626 }
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627
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628 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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629 # https://github.com/sneumann/xcms/issues/247
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630 c.XCMSnExp <- function(...) {
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631 .concatenate_XCMSnExp(...)
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632 }
32
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633
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634 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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635 # https://github.com/sneumann/xcms/issues/247
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636 c.MSnbase <- function(...) {
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637 .concatenate_OnDiskMSnExp(...)
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638 }