Mercurial > repos > lecorguille > xcms_retcor
annotate lib.r @ 23:faf4a6b67304 draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
author | workflow4metabolomics |
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date | Thu, 13 Feb 2020 06:43:08 -0500 |
parents | 972e76582173 |
children | c8011370e90f |
rev | line source |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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1 #@authors ABiMS TEAM, Y. Guitton |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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3 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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4 #@author G. Le Corguille |
8828cba9aedd
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 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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6 parseCommandArgs <- function(...) { |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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7 args <- batch::parseCommandArgs(...) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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8 for (key in names(args)) { |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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9 if (args[key] %in% c("TRUE","FALSE")) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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10 args[key] = as.logical(args[key]) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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11 } |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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12 return(args) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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13 } |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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14 |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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15 #@author G. Le Corguille |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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16 # This function will |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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17 # - load the packages |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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18 # - display the sessionInfo |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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19 loadAndDisplayPackages <- function(pkgs) { |
8828cba9aedd
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))) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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21 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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22 sessioninfo = sessionInfo() |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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23 cat(sessioninfo$R.version$version.string,"\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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24 cat("Main packages:\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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26 cat("Other loaded packages:\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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28 } |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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29 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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30 #@author G. Le Corguille |
8828cba9aedd
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. |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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32 mergeChrom <- function(chrom_merged, chrom) { |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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33 if (is.null(chrom_merged)) return(NULL) |
8828cba9aedd
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) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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35 return(chrom_merged) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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36 } |
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54cc3edfe35c
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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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39 # This function merge several xdata into one. |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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40 mergeXData <- function(args) { |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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41 chromTIC <- NULL |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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42 chromBPI <- NULL |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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43 chromTIC_adjusted <- NULL |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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44 chromBPI_adjusted <- NULL |
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972e76582173
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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45 md5sumList <- NULL |
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8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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46 for(image in args$images) { |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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47 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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48 load(image) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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49 # Handle infiles |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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50 if (!exists("singlefile")) singlefile <- NULL |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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51 if (!exists("zipfile")) zipfile <- NULL |
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972e76582173
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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52 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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53 zipfile <- rawFilePath$zipfile |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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54 singlefile <- rawFilePath$singlefile |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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55 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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56 if (exists("raw_data")) xdata <- raw_data |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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58 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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59 cat(sampleNamesList$sampleNamesOrigin,"\n") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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60 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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61 if (!exists("xdata_merged")) { |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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62 xdata_merged <- xdata |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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63 singlefile_merged <- singlefile |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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64 md5sumList_merged <- md5sumList |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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65 sampleNamesList_merged <- sampleNamesList |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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66 chromTIC_merged <- chromTIC |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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67 chromBPI_merged <- chromBPI |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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68 chromTIC_adjusted_merged <- chromTIC_adjusted |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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69 chromBPI_adjusted_merged <- chromBPI_adjusted |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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70 } else { |
8828cba9aedd
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) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4632d03b53c344757d71dd3310d37069fb498b26
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata) |
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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74 |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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75 singlefile_merged <- c(singlefile_merged,singlefile) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin) |
8828cba9aedd
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) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI) |
8828cba9aedd
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) |
8828cba9aedd
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) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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83 } |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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 } |
2
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125 |
7
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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 |
22
972e76582173
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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152 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") |
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153 names(group_colors) <- unique(xdata$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(length(unique(xdata$sample_group)), "Set1") |
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174 if (length(group_colors) > 1) { |
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175 names(group_colors) <- unique(xdata$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(length(unique(xdata$sample_group)), "Set1") |
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243 if (length(group_colors) > 1) { |
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244 names(group_colors) <- unique(xdata$sample_group) |
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245 plot(chrom, col = group_colors[as.factor(chrom$sample_group)], main=main, peakType = "none") |
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246 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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247 } |
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248 |
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249 # Color by sample |
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250 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main, peakType = "none") |
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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 will compute MD5 checksum to check the data integrity |
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321 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
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322 getMd5sum <- function (files) { |
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323 cat("Compute md5 checksum...\n") |
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324 library(tools) |
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325 return(as.matrix(md5sum(files))) |
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326 } |
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327 |
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328 # This function retrieve the raw file in the working directory |
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329 # - if zipfile: unzip the file with its directory tree |
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330 # - if singlefiles: set symlink with the good filename |
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331 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
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332 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile, args, prefix="") { |
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333 |
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334 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'") |
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335 |
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336 # single - if the file are passed in the command arguments -> refresh singlefile |
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337 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) { |
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338 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath",prefix)]],"\\|")) |
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339 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName",prefix)]],"\\|")) |
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340 |
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341 singlefile <- NULL |
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342 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { |
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343 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] |
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344 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] |
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345 # In case, an url is used to import data within Galaxy |
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346 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1) |
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347 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath |
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348 } |
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349 } |
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350 # zipfile - if the file are passed in the command arguments -> refresh zipfile |
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351 if (!is.null(args[[paste0("zipfile",prefix)]])) |
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352 zipfile <- args[[paste0("zipfile",prefix)]] |
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353 |
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354 # single |
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355 if(!is.null(singlefile) && (length("singlefile")>0)) { |
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356 files <- vector() |
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357 for (singlefile_sampleName in names(singlefile)) { |
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358 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]] |
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359 if(!file.exists(singlefile_galaxyPath)){ |
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360 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") |
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361 print(error_message); stop(error_message) |
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362 } |
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363 |
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364 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T))) |
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365 file.copy(singlefile_galaxyPath, singlefile_sampleName) |
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366 files <- c(files, singlefile_sampleName) |
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367 } |
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368 } |
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369 # zipfile |
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370 if(!is.null(zipfile) && (zipfile != "")) { |
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371 if(!file.exists(zipfile)){ |
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372 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") |
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373 print(error_message) |
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374 stop(error_message) |
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375 } |
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376 suppressWarnings(unzip(zipfile, unzip="unzip")) |
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377 |
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378 #get the directory name |
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379 suppressWarnings(filesInZip <- unzip(zipfile, list=T)) |
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380 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))) |
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381 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] |
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382 directory <- "." |
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383 if (length(directories) == 1) directory <- directories |
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384 |
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385 cat("files_root_directory\t",directory,"\n") |
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386 |
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387 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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388 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
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389 info <- file.info(directory) |
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390 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE) |
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391 files <- c(directory[!info$isdir], listed) |
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392 exists <- file.exists(files) |
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393 files <- files[exists] |
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394 |
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395 } |
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396 return(list(zipfile=zipfile, singlefile=singlefile, files=files)) |
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397 |
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398 } |
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399 |
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400 |
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401 # This function retrieve a xset like object |
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402 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
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403 getxcmsSetObject <- function(xobject) { |
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404 # XCMS 1.x |
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405 if (class(xobject) == "xcmsSet") |
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406 return (xobject) |
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407 # XCMS 3.x |
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408 if (class(xobject) == "XCMSnExp") { |
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409 # Get the legacy xcmsSet object |
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410 suppressWarnings(xset <- as(xobject, 'xcmsSet')) |
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411 if (!is.null(xset@phenoData$sample_group)) |
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412 sampclass(xset) <- xset@phenoData$sample_group |
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413 else |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
8
diff
changeset
|
414 sampclass(xset) <- "." |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
8
diff
changeset
|
415 return (xset) |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
8
diff
changeset
|
416 } |
8828cba9aedd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
8
diff
changeset
|
417 } |