Mercurial > repos > lecorguille > xcms_group
annotate lib.r @ 20:63d9c5980c07 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
author | lecorguille |
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date | Thu, 07 Mar 2019 07:40:20 -0500 |
parents | c8f8d598f562 |
children | 2d94a873d649 |
rev | line source |
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833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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1 #@authors ABiMS TEAM, Y. Guitton |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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3 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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4 #@author G. Le Corguille |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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5 # solve an issue with batch if arguments are logical TRUE/FALSE |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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6 parseCommandArgs <- function(...) { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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7 args <- batch::parseCommandArgs(...) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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8 for (key in names(args)) { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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9 if (args[key] %in% c("TRUE","FALSE")) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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10 args[key] = as.logical(args[key]) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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11 } |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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12 return(args) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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13 } |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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14 |
14
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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15 #@author G. Le Corguille |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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16 # This function will |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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17 # - load the packages |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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18 # - display the sessionInfo |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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19 loadAndDisplayPackages <- function(pkgs) { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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21 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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22 sessioninfo = sessionInfo() |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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23 cat(sessioninfo$R.version$version.string,"\n") |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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24 cat("Main packages:\n") |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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26 cat("Other loaded packages:\n") |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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28 } |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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29 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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30 #@author G. Le Corguille |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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31 # This function merge several chromBPI or chromTIC into one. |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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32 mergeChrom <- function(chrom_merged, chrom) { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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33 if (is.null(chrom_merged)) return(NULL) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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35 return(chrom_merged) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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36 } |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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37 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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38 #@author G. Le Corguille |
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833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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39 # This function merge several xdata into one. |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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40 mergeXData <- function(args) { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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41 chromTIC <- NULL |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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42 chromBPI <- NULL |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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43 chromTIC_adjusted <- NULL |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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44 chromBPI_adjusted <- NULL |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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45 for(image in args$images) { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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46 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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47 load(image) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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48 # Handle infiles |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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49 if (!exists("singlefile")) singlefile <- NULL |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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50 if (!exists("zipfile")) zipfile <- NULL |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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52 zipfile <- rawFilePath$zipfile |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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53 singlefile <- rawFilePath$singlefile |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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55 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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56 if (exists("raw_data")) xdata <- raw_data |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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58 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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59 cat(sampleNamesList$sampleNamesOrigin,"\n") |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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60 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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61 if (!exists("xdata_merged")) { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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62 xdata_merged <- xdata |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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63 singlefile_merged <- singlefile |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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64 md5sumList_merged <- md5sumList |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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65 sampleNamesList_merged <- sampleNamesList |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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66 chromTIC_merged <- chromTIC |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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67 chromBPI_merged <- chromBPI |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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68 chromTIC_adjusted_merged <- chromTIC_adjusted |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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69 chromBPI_adjusted_merged <- chromBPI_adjusted |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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70 } else { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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74 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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75 singlefile_merged <- c(singlefile_merged,singlefile) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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83 } |
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84 } |
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85 rm(image) |
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86 xdata <- xdata_merged; rm(xdata_merged) |
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87 singlefile <- singlefile_merged; rm(singlefile_merged) |
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged) |
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged) |
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90 |
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91 if (!is.null(args$sampleMetadata)) { |
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92 cat("\tXSET PHENODATA SETTING...\n") |
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93 sampleMetadataFile <- args$sampleMetadata |
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F) |
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)] |
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96 |
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97 if (any(is.na(pData(xdata)$sample_group))) { |
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)] |
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" ")) |
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100 print(error_message) |
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101 stop(error_message) |
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102 } |
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103 } |
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104 |
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData } |
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData } |
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107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData } |
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108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData } |
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109 |
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110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted)) |
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111 } |
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112 |
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113 #@author G. Le Corguille |
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114 # This function convert if it is required the Retention Time in minutes |
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) { |
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116 if (convertRTMinute){ |
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117 #converting the retention times (seconds) into minutes |
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118 print("converting the retention times into minutes in the variableMetadata") |
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60 |
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60 |
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60 |
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122 } |
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123 return (variableMetadata) |
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124 } |
4
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125 |
9
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126 #@author G. Le Corguille |
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127 # This function format ions identifiers |
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) { |
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_") |
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) |
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) |
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) |
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133 return(variableMetadata) |
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134 } |
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135 |
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136 #@author G. Le Corguille |
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137 # This function convert the remain NA to 0 in the dataMatrix |
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138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) { |
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139 if (naTOzero){ |
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140 dataMatrix[is.na(dataMatrix)] <- 0 |
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141 } |
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142 return (dataMatrix) |
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143 } |
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144 |
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145 #@author G. Le Corguille |
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146 # Draw the plotChromPeakDensity 3 per page in a pdf file |
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147 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) { |
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148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12) |
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149 |
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150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5)) |
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151 |
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152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] |
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153 names(group_colors) <- unique(xdata$sample_group) |
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154 |
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155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) |
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156 for (i in 1:nrow(featureDefinitions(xdata))) { |
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157 mzmin = featureDefinitions(xdata)[i,]$mzmin |
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158 mzmax = featureDefinitions(xdata)[i,]$mzmax |
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159 plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) |
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160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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161 } |
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162 |
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163 dev.off() |
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164 } |
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165 |
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166 #@author G. Le Corguille |
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167 # Draw the plotChromPeakDensity 3 per page in a pdf file |
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168 getPlotAdjustedRtime <- function(xdata) { |
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169 |
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170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12) |
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171 |
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172 # Color by group |
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173 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] |
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174 if (length(group_colors) > 1) { |
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175 names(group_colors) <- unique(xdata$sample_group) |
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176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group]) |
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177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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178 } |
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179 |
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180 # Color by sample |
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181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name))) |
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182 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1) |
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183 |
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184 dev.off() |
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185 } |
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186 |
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187 #@author G. Le Corguille |
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188 # value: intensity values to be used into, maxo or intb |
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189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) { |
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190 dataMatrix <- featureValues(xdata, method="medret", value=intval) |
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191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix))) |
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192 dataMatrix = cbind(name=groupnames(xdata), dataMatrix) |
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193 variableMetadata <- featureDefinitions(xdata) |
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194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" |
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195 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata) |
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196 |
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197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) |
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198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) |
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199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero) |
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200 |
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201 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export |
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202 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",") |
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203 |
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204 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) |
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205 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) |
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206 |
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207 } |
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208 |
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209 #@author G. Le Corguille |
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210 # It allow different of field separators |
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211 getDataFrameFromFile <- function(filename, header=T) { |
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212 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F) |
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213 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F) |
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214 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F) |
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215 if (ncol(myDataFrame) < 2) { |
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216 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation" |
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217 print(error_message) |
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218 stop(error_message) |
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219 } |
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220 return(myDataFrame) |
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221 } |
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222 |
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223 #@author G. Le Corguille |
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224 # Draw the BPI and TIC graphics |
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225 # colored by sample names or class names |
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226 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") { |
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227 |
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228 if (aggregationFun == "sum") |
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229 type="Total Ion Chromatograms" |
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230 else |
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231 type="Base Peak Intensity Chromatograms" |
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232 |
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233 adjusted="Raw" |
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234 if (hasAdjustedRtime(xdata)) |
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235 adjusted="Adjusted" |
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236 |
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237 main <- paste(type,":",adjusted,"data") |
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238 |
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239 pdf(pdfname, width=16, height=10) |
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240 |
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241 # Color by group |
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242 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] |
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243 if (length(group_colors) > 1) { |
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244 names(group_colors) <- unique(xdata$sample_group) |
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245 plot(chrom, col = group_colors[chrom$sample_group], main=main) |
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246 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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247 } |
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248 |
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249 # Color by sample |
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250 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main) |
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251 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1) |
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252 |
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253 dev.off() |
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254 } |
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255 |
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256 |
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257 # Get the polarities from all the samples of a condition |
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258 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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259 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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260 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") { |
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261 cat("Creating the sampleMetadata file...\n") |
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262 |
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263 #Create the sampleMetada dataframe |
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264 sampleMetadata <- xdata@phenoData@data |
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265 rownames(sampleMetadata) <- NULL |
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266 colnames(sampleMetadata) <- c("sample_name", "class") |
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267 |
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268 sampleNamesOrigin <- sampleMetadata$sample_name |
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269 sampleNamesMakeNames <- make.names(sampleNamesOrigin) |
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270 |
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271 if (any(duplicated(sampleNamesMakeNames))) { |
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272 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr()) |
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273 for (sampleName in sampleNamesOrigin) { |
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274 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) |
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275 } |
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276 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") |
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277 } |
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278 |
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279 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { |
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280 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n") |
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281 for (sampleName in sampleNamesOrigin) { |
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282 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) |
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283 } |
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284 } |
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285 |
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286 sampleMetadata$sample_name <- sampleNamesMakeNames |
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287 |
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288 |
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289 #For each sample file, the following actions are done |
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290 for (fileIdx in 1:length(fileNames(xdata))) { |
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291 #Check if the file is in the CDF format |
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292 if (!mzR:::netCDFIsFile(fileNames(xdata))) { |
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293 |
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294 # If the column isn't exist, with add one filled with NA |
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295 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA |
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296 |
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297 #Extract the polarity (a list of polarities) |
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298 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"] |
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299 #Verify if all the scans have the same polarity |
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300 uniq_list <- unique(polarity) |
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301 if (length(uniq_list)>1){ |
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302 polarity <- "mixed" |
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303 } else { |
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304 polarity <- as.character(uniq_list) |
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305 } |
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306 |
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307 #Set the polarity attribute |
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308 sampleMetadata$polarity[fileIdx] <- polarity |
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309 } |
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310 |
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311 } |
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312 |
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313 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) |
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314 |
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315 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames)) |
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316 |
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317 } |
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318 |
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319 |
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320 # This function check if xcms will found all the files |
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321 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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322 checkFilesCompatibilityWithXcms <- function(directory) { |
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323 cat("Checking files filenames compatibilities with xmcs...\n") |
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324 # WHAT XCMS WILL FIND |
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325 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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326 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
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327 info <- file.info(directory) |
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328 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) |
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329 files <- c(directory[!info$isdir], listed) |
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330 files_abs <- file.path(getwd(), files) |
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331 exists <- file.exists(files_abs) |
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332 files[exists] <- files_abs[exists] |
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333 files[exists] <- sub("//","/",files[exists]) |
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334 |
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335 # WHAT IS ON THE FILESYSTEM |
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336 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) |
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337 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] |
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338 |
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339 # COMPARISON |
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340 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { |
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341 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) |
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342 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) |
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343 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") |
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344 } |
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345 } |
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346 |
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347 |
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348 #This function list the compatible files within the directory as xcms did |
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349 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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350 getMSFiles <- function (directory) { |
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351 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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352 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
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353 info <- file.info(directory) |
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354 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE) |
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355 files <- c(directory[!info$isdir], listed) |
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356 exists <- file.exists(files) |
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357 files <- files[exists] |
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358 return(files) |
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359 } |
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360 |
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361 # This function check if XML contains special caracters. It also checks integrity and completness. |
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362 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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363 checkXmlStructure <- function (directory) { |
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364 cat("Checking XML structure...\n") |
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365 |
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366 cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;") |
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367 capture <- system(cmd, intern=TRUE) |
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368 |
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369 if (length(capture)>0){ |
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370 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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371 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr()) |
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372 write(capture, stderr()) |
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373 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files") |
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374 } |
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375 |
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376 } |
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377 |
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378 |
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379 # This function check if XML contain special characters |
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380 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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381 deleteXmlBadCharacters<- function (directory) { |
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382 cat("Checking Non ASCII characters in the XML...\n") |
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383 |
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384 processed <- F |
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385 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE) |
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386 for (i in l){ |
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387 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="") |
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388 capture <- suppressWarnings(system(cmd, intern=TRUE)) |
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389 if (length(capture)>0){ |
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390 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) |
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391 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") ) |
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392 c <- system(cmd, intern=TRUE) |
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393 capture <- "" |
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394 processed <- T |
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395 } |
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396 } |
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397 if (processed) cat("\n\n") |
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398 return(processed) |
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399 } |
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400 |
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401 |
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402 # This function will compute MD5 checksum to check the data integrity |
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403 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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404 getMd5sum <- function (directory) { |
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405 cat("Compute md5 checksum...\n") |
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406 # WHAT XCMS WILL FIND |
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407 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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408 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
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409 info <- file.info(directory) |
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410 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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411 files <- c(directory[!info$isdir], listed) |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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412 exists <- file.exists(files) |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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413 files <- files[exists] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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414 |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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415 library(tools) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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416 |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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417 #cat("\n\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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418 |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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419 return(as.matrix(md5sum(files))) |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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420 } |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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421 |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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422 |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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423 # This function get the raw file path from the arguments |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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424 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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425 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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426 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'") |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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427 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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428 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]] |
10
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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429 |
14
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430 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
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431 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]] |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
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432 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]] |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
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433 } |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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434 if (exists("singlefile_galaxyPaths")){ |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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435 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|")) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
|
436 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|")) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
|
437 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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438 singlefile <- NULL |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
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439 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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440 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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441 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
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442 # In case, an url is used to import data within Galaxy |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
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443 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
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444 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath |
10
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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445 } |
14
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446 } |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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447 return(list(zipfile=zipfile, singlefile=singlefile)) |
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c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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448 } |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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449 |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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450 # This function retrieve the raw file in the working directory |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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451 # - if zipfile: unzip the file with its directory tree |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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452 # - if singlefiles: set symlink with the good filename |
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833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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453 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
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c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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454 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) { |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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455 if(!is.null(singlefile) && (length("singlefile")>0)) { |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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456 for (singlefile_sampleName in names(singlefile)) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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457 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]] |
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c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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458 if(!file.exists(singlefile_galaxyPath)){ |
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833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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459 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") |
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c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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460 print(error_message); stop(error_message) |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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461 } |
4
2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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462 |
14
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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463 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T))) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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464 file.copy(singlefile_galaxyPath, singlefile_sampleName) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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465 |
10
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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466 } |
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467 directory <- "." |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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468 |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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469 } |
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833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
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470 if(!is.null(zipfile) && (zipfile != "")) { |
10
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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471 if(!file.exists(zipfile)){ |
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833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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472 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") |
10
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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473 print(error_message) |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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|
474 stop(error_message) |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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changeset
|
475 } |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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|
476 |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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|
477 #list all file in the zip file |
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833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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478 #zip_files <- unzip(zipfile,list=T)[,"Name"] |
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2db1d1d0f131
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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changeset
|
479 |
10
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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|
480 #unzip |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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481 suppressWarnings(unzip(zipfile, unzip="unzip")) |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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482 |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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|
483 #get the directory name |
14
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
|
484 suppressWarnings(filesInZip <- unzip(zipfile, list=T)) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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485 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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486 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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487 directory <- "." |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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changeset
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488 if (length(directories) == 1) directory <- directories |
10
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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changeset
|
489 |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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490 cat("files_root_directory\t",directory,"\n") |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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changeset
|
491 |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents:
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diff
changeset
|
492 } |
c81275aee959
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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parents:
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493 return (directory) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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494 } |
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833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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495 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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496 |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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497 # This function retrieve a xset like object |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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498 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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499 getxcmsSetObject <- function(xobject) { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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500 # XCMS 1.x |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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501 if (class(xobject) == "xcmsSet") |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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502 return (xobject) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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503 # XCMS 3.x |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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504 if (class(xobject) == "XCMSnExp") { |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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505 # Get the legacy xcmsSet object |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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506 suppressWarnings(xset <- as(xobject, 'xcmsSet')) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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507 if (!is.null(xset@phenoData$sample_group)) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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508 sampclass(xset) <- xset@phenoData$sample_group |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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509 else |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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510 sampclass(xset) <- "." |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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511 return (xset) |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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512 } |
833d2c821d9c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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513 } |