Mercurial > repos > lecorguille > xcms_xcmsset

annotate lib.r @ 15:b62808a2a008 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author lecorguille
date Tue, 18 Sep 2018 16:07:36 -0400
parents 15646e937936
children 517d4375db53
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15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
1 #@authors ABiMS TEAM, Y. Guitton
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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3
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
4 #@author G. Le Corguille
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
5 # solve an issue with batch if arguments are logical TRUE/FALSE
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
6 parseCommandArgs <- function(...) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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7 args <- batch::parseCommandArgs(...)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
8 for (key in names(args)) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
9 if (args[key] %in% c("TRUE","FALSE"))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
10 args[key] = as.logical(args[key])
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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11 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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12 return(args)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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13 }
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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14
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
15 #@author G. Le Corguille
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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16 # This function will
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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17 # - load the packages
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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18 # - display the sessionInfo
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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19 loadAndDisplayPackages <- function(pkgs) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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21
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
22 sessioninfo = sessionInfo()
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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23 cat(sessioninfo$R.version$version.string,"\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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24 cat("Main packages:\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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26 cat("Other loaded packages:\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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28 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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29
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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30 #@author G. Le Corguille
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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31 # This function merge several chromBPI or chromTIC into one.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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32 mergeChrom <- function(chrom_merged, chrom) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
33 if (is.null(chrom_merged)) return(NULL)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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35 return(chrom_merged)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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36 }
6
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37
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 6
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38 #@author G. Le Corguille
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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39 # This function merge several xdata into one.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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40 mergeXData <- function(args) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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41 chromTIC <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
42 chromBPI <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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43 chromTIC_adjusted <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
44 chromBPI_adjusted <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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45 for(image in args$images) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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46
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lecorguille
parents: 12
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47 load(image)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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48 # Handle infiles
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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49 if (!exists("singlefile")) singlefile <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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50 if (!exists("zipfile")) zipfile <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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52 zipfile <- rawFilePath$zipfile
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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53 singlefile <- rawFilePath$singlefile
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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55
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lecorguille
parents: 12
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56 if (exists("raw_data")) xdata <- raw_data
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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parents: 12
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58
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lecorguille
parents: 12
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59 cat(sampleNamesList$sampleNamesOrigin,"\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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60
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lecorguille
parents: 12
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61 if (!exists("xdata_merged")) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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62 xdata_merged <- xdata
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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63 singlefile_merged <- singlefile
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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64 md5sumList_merged <- md5sumList
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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65 sampleNamesList_merged <- sampleNamesList
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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66 chromTIC_merged <- chromTIC
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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67 chromBPI_merged <- chromBPI
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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68 chromTIC_adjusted_merged <- chromTIC_adjusted
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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69 chromBPI_adjusted_merged <- chromBPI_adjusted
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
70 } else {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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74
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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75 singlefile_merged <- c(singlefile_merged,singlefile)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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83 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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84 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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85 rm(image)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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86 xdata <- xdata_merged; rm(xdata_merged)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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87 singlefile <- singlefile_merged; rm(singlefile_merged)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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90
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91 if (!is.null(args$sampleMetadata)) {
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lecorguille
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92 cat("\tXSET PHENODATA SETTING...\n")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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93 sampleMetadataFile <- args$sampleMetadata
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
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96
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97 if (any(is.na(pData(xdata)$sample_group))) {
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
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100 print(error_message)
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101 stop(error_message)
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102 }
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103 }
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104
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
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107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
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108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
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109
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110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
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111 }
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112
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113 #@author G. Le Corguille
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114 # This function convert if it is required the Retention Time in minutes
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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116 if (convertRTMinute){
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117 #converting the retention times (seconds) into minutes
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118 print("converting the retention times into minutes in the variableMetadata")
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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122 }
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123 return (variableMetadata)
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124 }
6
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125
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126 #@author G. Le Corguille
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127 # This function format ions identifiers
12
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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133 return(variableMetadata)
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134 }
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135
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136 #@author G. Le Corguille
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137 # This function convert the remain NA to 0 in the dataMatrix
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138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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139 if (naTOzero){
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140 dataMatrix[is.na(dataMatrix)] <- 0
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141 }
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142 return (dataMatrix)
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143 }
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144
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145 #@author G. Le Corguille
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146 # Draw the plotChromPeakDensity 3 per page in a pdf file
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147 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
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148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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149
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150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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151
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152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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153 names(group_colors) <- unique(xdata$sample_group)
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154
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155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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156 for (i in 1:nrow(featureDefinitions(xdata))) {
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157 mzmin = featureDefinitions(xdata)[i,]$mzmin
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158 mzmax = featureDefinitions(xdata)[i,]$mzmax
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159 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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161 }
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162
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163 dev.off()
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164 }
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165
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166 #@author G. Le Corguille
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167 # Draw the plotChromPeakDensity 3 per page in a pdf file
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168 getPlotAdjustedRtime <- function(xdata) {
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169
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170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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171
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172 # Color by group
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173 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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174 if (length(group_colors) > 1) {
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175 names(group_colors) <- unique(xdata$sample_group)
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176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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178 }
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179
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180 # Color by sample
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181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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182 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
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183
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184 dev.off()
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185 }
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186
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187 #@author G. Le Corguille
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188 # value: intensity values to be used into, maxo or intb
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189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput) {
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190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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191 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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192 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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193 variableMetadata <- featureDefinitions(xdata)
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194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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195 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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196
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197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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200
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201 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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202 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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203
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204 }
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205
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206 #@author G. Le Corguille
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207 # It allow different of field separators
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208 getDataFrameFromFile <- function(filename, header=T) {
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209 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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210 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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211 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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212 if (ncol(myDataFrame) < 2) {
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213 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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214 print(error_message)
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215 stop(error_message)
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216 }
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217 return(myDataFrame)
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218 }
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219
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220 #@author G. Le Corguille
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221 # Draw the BPI and TIC graphics
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222 # colored by sample names or class names
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223 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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224
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225 if (aggregationFun == "sum")
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226 type="Total Ion Chromatograms"
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227 else
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228 type="Base Peak Intensity Chromatograms"
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229
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230 adjusted="Raw"
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231 if (hasAdjustedRtime(xdata))
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232 adjusted="Adjusted"
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233
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234 main <- paste(type,":",adjusted,"data")
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235
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236 pdf(pdfname, width=16, height=10)
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237
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238 # Color by group
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239 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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240 if (length(group_colors) > 1) {
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241 names(group_colors) <- unique(xdata$sample_group)
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242 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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243 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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244 }
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245
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246 # Color by sample
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247 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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248 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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249
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250 dev.off()
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251 }
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252
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253
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254 # Get the polarities from all the samples of a condition
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255 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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256 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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257 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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258 cat("Creating the sampleMetadata file...\n")
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259
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260 #Create the sampleMetada dataframe
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261 sampleMetadata <- xdata@phenoData@data
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262 rownames(sampleMetadata) <- NULL
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263 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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264
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265 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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266 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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267
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268 if (any(duplicated(sampleNamesMakeNames))) {
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269 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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270 for (sampleName in sampleNamesOrigin) {
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271 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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272 }
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273 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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274 }
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275
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276 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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277 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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278 for (sampleName in sampleNamesOrigin) {
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279 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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280 }
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281 }
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282
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283 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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284
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285
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286 #For each sample file, the following actions are done
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287 for (fileIdx in 1:length(fileNames(xdata))) {
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288 #Check if the file is in the CDF format
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289 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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290
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291 # If the column isn't exist, with add one filled with NA
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292 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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293
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294 #Extract the polarity (a list of polarities)
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295 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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296 #Verify if all the scans have the same polarity
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297 uniq_list <- unique(polarity)
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298 if (length(uniq_list)>1){
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299 polarity <- "mixed"
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300 } else {
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301 polarity <- as.character(uniq_list)
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302 }
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303
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304 #Set the polarity attribute
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305 sampleMetadata$polarity[fileIdx] <- polarity
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306 }
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307
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308 }
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309
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310 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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311
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312 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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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 check if xcms will found all the files
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318 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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319 checkFilesCompatibilityWithXcms <- function(directory) {
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320 cat("Checking files filenames compatibilities with xmcs...\n")
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321 # WHAT XCMS WILL FIND
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322 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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323 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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324 info <- file.info(directory)
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325 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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326 files <- c(directory[!info$isdir], listed)
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327 files_abs <- file.path(getwd(), files)
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328 exists <- file.exists(files_abs)
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329 files[exists] <- files_abs[exists]
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330 files[exists] <- sub("//","/",files[exists])
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331
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332 # WHAT IS ON THE FILESYSTEM
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333 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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334 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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335
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336 # COMPARISON
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337 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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338 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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339 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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340 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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341 }
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342 }
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343
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344
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345 #This function list the compatible files within the directory as xcms did
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346 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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347 getMSFiles <- function (directory) {
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348 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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349 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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350 info <- file.info(directory)
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351 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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352 files <- c(directory[!info$isdir], listed)
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353 exists <- file.exists(files)
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354 files <- files[exists]
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355 return(files)
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356 }
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357
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358 # This function check if XML contains special caracters. It also checks integrity and completness.
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359 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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360 checkXmlStructure <- function (directory) {
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361 cat("Checking XML structure...\n")
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362
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363 cmd <- paste0("IFS=$'\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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364 capture <- system(cmd, intern=TRUE)
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365
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366 if (length(capture)>0){
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367 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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368 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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369 write(capture, stderr())
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370 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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371 }
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372
6
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373 }
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374
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375
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376 # This function check if XML contain special characters
6
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377 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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378 deleteXmlBadCharacters<- function (directory) {
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15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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379 cat("Checking Non ASCII characters in the XML...\n")
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380
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381 processed <- F
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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382 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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383 for (i in l){
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384 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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385 capture <- suppressWarnings(system(cmd, intern=TRUE))
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15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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386 if (length(capture)>0){
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387 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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388 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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389 c <- system(cmd, intern=TRUE)
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390 capture <- ""
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391 processed <- T
12
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392 }
6
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393 }
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394 if (processed) cat("\n\n")
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395 return(processed)
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396 }
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397
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398
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399 # This function will compute MD5 checksum to check the data integrity
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400 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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401 getMd5sum <- function (directory) {
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lecorguille
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402 cat("Compute md5 checksum...\n")
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lecorguille
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403 # WHAT XCMS WILL FIND
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lecorguille
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404 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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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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405 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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406 info <- file.info(directory)
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407 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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408 files <- c(directory[!info$isdir], listed)
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409 exists <- file.exists(files)
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diff changeset
410 files <- files[exists]
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lecorguille
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diff changeset
411
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lecorguille
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412 library(tools)
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diff changeset
413
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414 #cat("\n\n")
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lecorguille
parents: 11
diff changeset
415
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416 return(as.matrix(md5sum(files)))
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lecorguille
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417 }
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lecorguille
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diff changeset
418
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lecorguille
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diff changeset
419
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420 # This function get the raw file path from the arguments
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lecorguille
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421 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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lecorguille
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422 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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423 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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diff changeset
424
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425 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
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diff changeset
426
15
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diff changeset
427 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
428 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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diff changeset
429 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
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lecorguille
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diff changeset
430 }
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lecorguille
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diff changeset
431 if (exists("singlefile_galaxyPaths")){
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
432 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
433 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
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lecorguille
parents: 12
diff changeset
434
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diff changeset
435 singlefile <- NULL
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lecorguille
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diff changeset
436 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
437 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
438 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
439 # In case, an url is used to import data within Galaxy
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
440 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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diff changeset
441 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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lecorguille
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diff changeset
442 }
15
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lecorguille
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diff changeset
443 }
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lecorguille
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diff changeset
444 return(list(zipfile=zipfile, singlefile=singlefile))
12
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lecorguille
parents: 11
diff changeset
445 }
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
446
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
447 # This function retrieve the raw file in the working directory
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
448 # - if zipfile: unzip the file with its directory tree
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
449 # - if singlefiles: set symlink with the good filename
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lecorguille
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diff changeset
450 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
12
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lecorguille
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diff changeset
451 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
452 if(!is.null(singlefile) && (length("singlefile")>0)) {
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
453 for (singlefile_sampleName in names(singlefile)) {
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
454 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
455 if(!file.exists(singlefile_galaxyPath)){
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
456 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
457 print(error_message); stop(error_message)
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
458 }
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
459
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
460 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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461 file.copy(singlefile_galaxyPath, singlefile_sampleName)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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462
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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463 }
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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464 directory <- "."
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15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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465
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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466 }
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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467 if(!is.null(zipfile) && (zipfile != "")) {
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15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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468 if(!file.exists(zipfile)){
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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469 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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470 print(error_message)
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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471 stop(error_message)
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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472 }
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
473
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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474 #list all file in the zip file
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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475 #zip_files <- unzip(zipfile,list=T)[,"Name"]
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0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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476
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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477 #unzip
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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478 suppressWarnings(unzip(zipfile, unzip="unzip"))
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
479
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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480 #get the directory name
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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481 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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482 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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483 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
484 directory <- "."
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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485 if (length(directories) == 1) directory <- directories
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15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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486
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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487 cat("files_root_directory\t",directory,"\n")
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
488
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
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489 }
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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490 return (directory)
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lecorguille
parents:
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491 }
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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492
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lecorguille
parents: 12
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493
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lecorguille
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494 # This function retrieve a xset like object
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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495 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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lecorguille
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496 getxcmsSetObject <- function(xobject) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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497 # XCMS 1.x
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lecorguille
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498 if (class(xobject) == "xcmsSet")
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lecorguille
parents: 12
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499 return (xobject)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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500 # XCMS 3.x
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lecorguille
parents: 12
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501 if (class(xobject) == "XCMSnExp") {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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502 # Get the legacy xcmsSet object
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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503 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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lecorguille
parents: 12
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504 if (!is.null(xset@phenoData$sample_group))
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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505 sampclass(xset) <- xset@phenoData$sample_group
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
506 else
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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507 sampclass(xset) <- "."
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lecorguille
parents: 12
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508 return (xset)
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lecorguille
parents: 12
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509 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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510 }