Mercurial > repos > lecorguille > xcms_merge
annotate lib.r @ 9:35b9bb3205d8 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1444e7c7ebd2bb5bdadede71c60a39f560721a98
author | lecorguille |
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date | Mon, 05 Mar 2018 09:31:22 -0500 |
parents | 6b5504f877ff |
children | 47e953d9da82 |
rev | line source |
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dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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1 #@authors ABiMS TEAM, Y. Guitton |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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3 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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4 #@author G. Le Corguille |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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6 parseCommandArgs <- function(...) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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7 args <- batch::parseCommandArgs(...) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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8 for (key in names(args)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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9 if (args[key] %in% c("TRUE","FALSE")) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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10 args[key] = as.logical(args[key]) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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11 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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12 return(args) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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13 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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14 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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15 #@author G. Le Corguille |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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16 # This function will |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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17 # - load the packages |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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18 # - display the sessionInfo |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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19 loadAndDisplayPackages <- function(pkgs) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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21 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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22 sessioninfo = sessionInfo() |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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23 cat(sessioninfo$R.version$version.string,"\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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24 cat("Main packages:\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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26 cat("Other loaded packages:\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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28 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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29 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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30 #@author G. Le Corguille |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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31 # This function convert if it is required the Retention Time in minutes |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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32 RTSecondToMinute <- function(variableMetadata, convertRTMinute) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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33 if (convertRTMinute){ |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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34 #converting the retention times (seconds) into minutes |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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35 print("converting the retention times into minutes in the variableMetadata") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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36 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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37 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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38 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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39 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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40 return (variableMetadata) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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41 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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42 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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43 #@author G. Le Corguille |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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44 # This function format ions identifiers |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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45 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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46 splitDeco <- strsplit(as.character(variableMetadata$name),"_") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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47 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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48 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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49 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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50 return(variableMetadata) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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51 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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52 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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53 #@author G. Le Corguille |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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54 # Draw the plotChromPeakDensity 3 per page in a pdf file |
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6b5504f877ff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
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55 getPlotChromPeakDensity <- function(xdata, mzdigit=4) { |
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dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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56 pdf(file="plotChromPeakDensity.pdf", width=16, height=12) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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57 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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58 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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59 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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60 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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61 names(group_colors) <- unique(xdata$sample_group) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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62 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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63 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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64 for (i in 1:nrow(featureDefinitions(xdata))) { |
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6b5504f877ff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
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65 mzmin = featureDefinitions(xdata)[i,]$mzmin |
6b5504f877ff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
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66 mzmax = featureDefinitions(xdata)[i,]$mzmax |
6b5504f877ff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
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67 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) |
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dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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68 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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69 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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70 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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71 dev.off() |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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72 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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73 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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74 #@author G. Le Corguille |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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75 # Draw the plotChromPeakDensity 3 per page in a pdf file |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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76 getPlotAdjustedRtime <- function(xdata) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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77 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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78 # Color by group |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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79 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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80 names(group_colors) <- unique(xdata$sample_group) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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81 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group]) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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82 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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83 # Color by sample |
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84 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name))) |
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85 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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86 dev.off() |
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87 } |
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88 |
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89 #@author G. Le Corguille |
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90 # value: intensity values to be used into, maxo or intb |
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91 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) { |
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92 dataMatrix <- featureValues(xdata, method="medret", value=intval) |
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93 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix)) |
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94 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix) |
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95 variableMetadata <- featureDefinitions(xdata) |
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96 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" |
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97 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata) |
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98 |
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99 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) |
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100 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) |
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101 |
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102 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) |
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103 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) |
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104 |
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105 } |
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106 |
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107 #@author Y. Guitton |
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108 getBPC <- function(file,rtcor=NULL, ...) { |
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109 object <- xcmsRaw(file) |
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110 sel <- profRange(object, ...) |
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111 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE])) |
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112 #plotChrom(xcmsRaw(file), base=T) |
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113 } |
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114 |
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115 #@author Y. Guitton |
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116 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) { |
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117 cat("Creating BIC pdf...\n") |
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118 |
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119 if (is.null(xcmsSet)) { |
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120 cat("Enter an xcmsSet \n") |
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121 stop() |
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122 } else { |
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123 files <- filepaths(xcmsSet) |
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124 } |
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125 |
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126 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class |
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127 |
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128 classnames <- vector("list",length(phenoDataClass)) |
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129 for (i in 1:length(phenoDataClass)){ |
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130 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i]) |
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131 } |
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132 |
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133 N <- dim(phenoData(xcmsSet))[1] |
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134 |
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135 TIC <- vector("list",N) |
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136 |
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137 |
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138 for (j in 1:N) { |
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139 |
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140 TIC[[j]] <- getBPC(files[j]) |
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141 #good for raw |
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142 # seems strange for corrected |
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143 #errors if scanrange used in xcmsSetgeneration |
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144 if (!is.null(xcmsSet) && rt == "corrected") |
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145 rtcor <- xcmsSet@rt$corrected[[j]] |
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146 else |
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147 rtcor <- NULL |
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148 |
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149 TIC[[j]] <- getBPC(files[j],rtcor=rtcor) |
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150 # TIC[[j]][,1]<-rtcor |
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151 } |
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152 |
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153 |
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154 |
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155 pdf(pdfname,w=16,h=10) |
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156 cols <- rainbow(N) |
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157 lty <- 1:N |
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158 pch <- 1:N |
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159 #search for max x and max y in BPCs |
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160 xlim <- range(sapply(TIC, function(x) range(x[,1]))) |
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161 ylim <- range(sapply(TIC, function(x) range(x[,2]))) |
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162 ylim <- c(-ylim[2], ylim[2]) |
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163 |
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164 |
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165 ##plot start |
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166 |
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167 if (length(phenoDataClass)>2){ |
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168 for (k in 1:(length(phenoDataClass)-1)){ |
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169 for (l in (k+1):length(phenoDataClass)){ |
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170 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" ")) |
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171 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC") |
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172 colvect <- NULL |
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173 for (j in 1:length(classnames[[k]])) { |
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174 tic <- TIC[[classnames[[k]][j]]] |
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175 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") |
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176 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") |
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177 colvect <- append(colvect,cols[classnames[[k]][j]]) |
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178 } |
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179 for (j in 1:length(classnames[[l]])) { |
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180 # i <- class2names[j] |
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181 tic <- TIC[[classnames[[l]][j]]] |
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182 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l") |
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183 colvect <- append(colvect,cols[classnames[[l]][j]]) |
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184 } |
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185 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch) |
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186 } |
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187 } |
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188 }#end if length >2 |
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189 |
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190 if (length(phenoDataClass)==2){ |
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191 k <- 1 |
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192 l <- 2 |
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193 colvect <- NULL |
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194 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC") |
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195 |
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196 for (j in 1:length(classnames[[k]])) { |
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197 |
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198 tic <- TIC[[classnames[[k]][j]]] |
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199 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") |
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200 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") |
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201 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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202 } |
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203 for (j in 1:length(classnames[[l]])) { |
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204 # i <- class2names[j] |
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205 tic <- TIC[[classnames[[l]][j]]] |
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206 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l") |
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207 colvect <- append(colvect,cols[classnames[[l]][j]]) |
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208 } |
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209 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch) |
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210 |
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211 }#end length ==2 |
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212 |
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213 #case where only one class |
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214 if (length(phenoDataClass)==1){ |
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215 k <- 1 |
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216 ylim <- range(sapply(TIC, function(x) range(x[,2]))) |
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217 colvect <- NULL |
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218 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="BPC") |
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219 |
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220 for (j in 1:length(classnames[[k]])) { |
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221 tic <- TIC[[classnames[[k]][j]]] |
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222 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") |
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223 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") |
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224 colvect <- append(colvect,cols[classnames[[k]][j]]) |
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225 } |
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226 |
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227 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch) |
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228 |
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229 }#end length ==1 |
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230 |
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231 dev.off() #pdf(pdfname,w=16,h=10) |
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232 |
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233 invisible(TIC) |
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234 } |
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235 |
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236 |
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237 |
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238 #@author Y. Guitton |
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239 getTIC <- function(file, rtcor=NULL) { |
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240 object <- xcmsRaw(file) |
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241 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object, mzrange=range(object@env$mz))$intensity) |
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242 } |
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243 |
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244 #overlay TIC from all files in current folder or from xcmsSet, create pdf |
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245 #@author Y. Guitton |
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246 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf", rt=c("raw","corrected")) { |
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247 cat("Creating TIC pdf...\n") |
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248 |
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249 if (is.null(xcmsSet)) { |
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250 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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251 filepattern <- paste(paste("\\.", filepattern, "$", sep=""), collapse="|") |
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252 if (is.null(files)) |
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253 files <- getwd() |
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254 info <- file.info(files) |
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255 listed <- list.files(files[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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256 files <- c(files[!info$isdir], listed) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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257 } else { |
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258 files <- filepaths(xcmsSet) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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259 } |
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260 |
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261 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class |
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262 classnames <- vector("list",length(phenoDataClass)) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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263 for (i in 1:length(phenoDataClass)){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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264 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i]) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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265 } |
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266 |
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267 N <- length(files) |
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268 TIC <- vector("list",N) |
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269 |
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270 for (i in 1:N) { |
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271 if (!is.null(xcmsSet) && rt == "corrected") |
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272 rtcor <- xcmsSet@rt$corrected[[i]] else |
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273 rtcor <- NULL |
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274 TIC[[i]] <- getTIC(files[i], rtcor=rtcor) |
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275 } |
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276 |
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277 pdf(pdfname, w=16, h=10) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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278 cols <- rainbow(N) |
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279 lty <- 1:N |
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280 pch <- 1:N |
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281 #search for max x and max y in TICs |
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282 xlim <- range(sapply(TIC, function(x) range(x[,1]))) |
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283 ylim <- range(sapply(TIC, function(x) range(x[,2]))) |
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284 ylim <- c(-ylim[2], ylim[2]) |
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285 |
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286 |
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287 ##plot start |
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288 if (length(phenoDataClass)>2){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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289 for (k in 1:(length(phenoDataClass)-1)){ |
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290 for (l in (k+1):length(phenoDataClass)){ |
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291 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" ")) |
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292 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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293 colvect <- NULL |
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294 for (j in 1:length(classnames[[k]])) { |
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295 tic <- TIC[[classnames[[k]][j]]] |
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296 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") |
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297 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") |
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298 colvect <- append(colvect,cols[classnames[[k]][j]]) |
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299 } |
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300 for (j in 1:length(classnames[[l]])) { |
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301 # i=class2names[j] |
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302 tic <- TIC[[classnames[[l]][j]]] |
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303 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l") |
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304 colvect <- append(colvect,cols[classnames[[l]][j]]) |
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305 } |
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306 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch) |
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307 } |
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308 } |
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309 }#end if length >2 |
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310 if (length(phenoDataClass)==2){ |
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311 k <- 1 |
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312 l <- 2 |
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313 |
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314 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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315 colvect <- NULL |
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316 for (j in 1:length(classnames[[k]])) { |
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317 tic <- TIC[[classnames[[k]][j]]] |
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318 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") |
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319 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") |
dca722aecb67
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320 colvect <- append(colvect,cols[classnames[[k]][j]]) |
dca722aecb67
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321 } |
dca722aecb67
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322 for (j in 1:length(classnames[[l]])) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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323 # i <- class2names[j] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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324 tic <- TIC[[classnames[[l]][j]]] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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325 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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326 colvect <- append(colvect,cols[classnames[[l]][j]]) |
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327 } |
dca722aecb67
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328 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch) |
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329 |
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330 }#end length ==2 |
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331 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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332 #case where only one class |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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333 if (length(phenoDataClass)==1){ |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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334 k <- 1 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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335 ylim <- range(sapply(TIC, function(x) range(x[,2]))) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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336 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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337 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="TIC") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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338 colvect <- NULL |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff
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339 for (j in 1:length(classnames[[k]])) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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340 tic <- TIC[[classnames[[k]][j]]] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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341 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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342 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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343 colvect <- append(colvect,cols[classnames[[k]][j]]) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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344 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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345 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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346 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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347 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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348 }#end length ==1 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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349 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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350 dev.off() #pdf(pdfname,w=16,h=10) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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351 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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352 invisible(TIC) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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353 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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354 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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355 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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356 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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357 # Get the polarities from all the samples of a condition |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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358 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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359 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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360 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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361 cat("Creating the sampleMetadata file...\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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362 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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363 #Create the sampleMetada dataframe |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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364 sampleMetadata <- xdata@phenoData@data |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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365 rownames(sampleMetadata) <- NULL |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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366 colnames(sampleMetadata) <- c("sampleMetadata", "class") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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367 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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368 sampleNamesOrigin <- sampleMetadata$sampleMetadata |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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369 sampleNamesMakeNames <- make.names(sampleNamesOrigin) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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370 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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371 if (any(duplicated(sampleNamesMakeNames))) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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372 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()) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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373 for (sampleName in sampleNamesOrigin) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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374 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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375 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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376 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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377 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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378 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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379 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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380 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") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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381 for (sampleName in sampleNamesOrigin) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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382 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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383 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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384 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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385 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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386 sampleMetadata$sampleMetadata <- sampleNamesMakeNames |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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387 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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388 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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389 #For each sample file, the following actions are done |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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390 for (fileIdx in 1:length(fileNames(xdata))) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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391 #Check if the file is in the CDF format |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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392 if (!mzR:::netCDFIsFile(fileNames(xdata))) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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393 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
diff
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394 # If the column isn't exist, with add one filled with NA |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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395 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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396 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
diff
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397 #Extract the polarity (a list of polarities) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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398 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
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399 #Verify if all the scans have the same polarity |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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400 uniq_list <- unique(polarity) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
401 if (length(uniq_list)>1){ |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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402 polarity <- "mixed" |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
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|
403 } else { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
404 polarity <- as.character(uniq_list) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
405 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
406 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
407 #Set the polarity attribute |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
408 sampleMetadata$polarity[fileIdx] <- polarity |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
409 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
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|
410 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
411 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
412 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
413 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
414 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
415 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
416 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
417 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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changeset
|
418 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
419 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
420 # This function check if xcms will found all the files |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
421 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
422 checkFilesCompatibilityWithXcms <- function(directory) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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423 cat("Checking files filenames compatibilities with xmcs...\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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424 # WHAT XCMS WILL FIND |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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425 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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426 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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427 info <- file.info(directory) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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428 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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429 files <- c(directory[!info$isdir], listed) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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430 files_abs <- file.path(getwd(), files) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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431 exists <- file.exists(files_abs) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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432 files[exists] <- files_abs[exists] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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433 files[exists] <- sub("//","/",files[exists]) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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434 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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435 # WHAT IS ON THE FILESYSTEM |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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436 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) |
7
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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437 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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438 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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439 # COMPARISON |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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440 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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441 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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442 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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443 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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444 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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445 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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446 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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447 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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448 #This function list the compatible files within the directory as xcms did |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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449 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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450 getMSFiles <- function (directory) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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451 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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452 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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453 info <- file.info(directory) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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454 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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455 files <- c(directory[!info$isdir], listed) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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456 exists <- file.exists(files) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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457 files <- files[exists] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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458 return(files) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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459 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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460 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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461 # This function check if XML contains special caracters. It also checks integrity and completness. |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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462 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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463 checkXmlStructure <- function (directory) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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464 cat("Checking XML structure...\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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465 |
8
6b5504f877ff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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466 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;") |
7
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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467 capture <- system(cmd, intern=TRUE) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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468 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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469 if (length(capture)>0){ |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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470 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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471 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr()) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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472 write(capture, stderr()) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
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473 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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474 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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|
475 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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476 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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changeset
|
477 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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478 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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479 # This function check if XML contain special characters |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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480 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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481 deleteXmlBadCharacters<- function (directory) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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482 cat("Checking Non ASCII characters in the XML...\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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|
483 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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484 processed <- F |
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6b5504f877ff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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485 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE) |
7
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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486 for (i in l){ |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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487 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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488 capture <- suppressWarnings(system(cmd, intern=TRUE)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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489 if (length(capture)>0){ |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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490 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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491 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") ) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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492 c <- system(cmd, intern=TRUE) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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493 capture <- "" |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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494 processed <- T |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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|
495 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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|
496 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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497 if (processed) cat("\n\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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498 return(processed) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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499 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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500 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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|
501 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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502 # This function will compute MD5 checksum to check the data integrity |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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changeset
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503 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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changeset
|
504 getMd5sum <- function (directory) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
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changeset
|
505 cat("Compute md5 checksum...\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
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changeset
|
506 # WHAT XCMS WILL FIND |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
507 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
508 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
509 info <- file.info(directory) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
510 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
511 files <- c(directory[!info$isdir], listed) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
512 exists <- file.exists(files) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
513 files <- files[exists] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
514 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
515 library(tools) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
516 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
517 #cat("\n\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
518 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
519 return(as.matrix(md5sum(files))) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
520 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
521 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
522 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
523 # This function get the raw file path from the arguments |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
524 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
525 getRawfilePathFromArguments <- function(singlefile, zipfile, args) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
526 if (!is.null(args$zipfile)) zipfile <- args$zipfile |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
527 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
528 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
529 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
530 if (!is.null(args$singlefile_galaxyPath)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
531 singlefile_galaxyPaths <- args$singlefile_galaxyPath; |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
532 singlefile_sampleNames <- args$singlefile_sampleName |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
533 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
534 if (!is.null(args$singlefile_galaxyPathPositive)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
535 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive; |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
536 singlefile_sampleNames <- args$singlefile_sampleNamePositive |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
537 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
538 if (!is.null(args$singlefile_galaxyPathNegative)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
539 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative; |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
540 singlefile_sampleNames <- args$singlefile_sampleNameNegative |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
541 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
542 if (exists("singlefile_galaxyPaths")){ |
8
6b5504f877ff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents:
7
diff
changeset
|
543 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|")) |
6b5504f877ff
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
lecorguille
parents:
7
diff
changeset
|
544 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|")) |
7
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
545 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
546 singlefile <- NULL |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
547 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
548 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
549 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
550 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
551 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
552 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
553 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
554 args[[argument]] <- NULL |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
555 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
556 return(list(zipfile=zipfile, singlefile=singlefile, args=args)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
557 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
558 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
559 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
560 # This function retrieve the raw file in the working directory |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
561 # - if zipfile: unzip the file with its directory tree |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
562 # - if singlefiles: set symlink with the good filename |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
563 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
564 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
565 if(!is.null(singlefile) && (length("singlefile")>0)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
566 for (singlefile_sampleName in names(singlefile)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
567 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
568 if(!file.exists(singlefile_galaxyPath)){ |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
569 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
570 print(error_message); stop(error_message) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
571 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
572 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
573 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T))) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
574 file.copy(singlefile_galaxyPath, singlefile_sampleName) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
575 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
576 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
577 directory <- "." |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
578 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
579 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
580 if(!is.null(zipfile) && (zipfile != "")) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
581 if(!file.exists(zipfile)){ |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
582 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
583 print(error_message) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
584 stop(error_message) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
585 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
586 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
587 #list all file in the zip file |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
588 #zip_files <- unzip(zipfile,list=T)[,"Name"] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
589 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
590 #unzip |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
591 suppressWarnings(unzip(zipfile, unzip="unzip")) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
592 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
593 #get the directory name |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
594 suppressWarnings(filesInZip <- unzip(zipfile, list=T)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
595 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
596 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
597 directory <- "." |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
598 if (length(directories) == 1) directory <- directories |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
599 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
600 cat("files_root_directory\t",directory,"\n") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
601 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
602 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
603 return (directory) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
604 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
605 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
606 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
607 # This function retrieve a xset like object |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
608 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
609 getxcmsSetObject <- function(xobject) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
610 # XCMS 1.x |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
611 if (class(xobject) == "xcmsSet") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
612 return (xobject) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
613 # XCMS 3.x |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
614 if (class(xobject) == "XCMSnExp") { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
615 # Get the legacy xcmsSet object |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
616 suppressWarnings(xset <- as(xobject, 'xcmsSet')) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
617 sampclass(xset) <- xset@phenoData$sample_group |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
618 return (xset) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
619 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
620 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
621 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
622 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
623 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
624 # https://github.com/sneumann/xcms/issues/250 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
625 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
626 mzfmt <- paste("%.", mzdec, "f", sep = "") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
627 rtfmt <- paste("%.", rtdec, "f", sep = "") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
628 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
629 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T", |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
630 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
631 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
632 if (any(dup <- duplicated(gnames))) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
633 for (dupname in unique(gnames[dup])) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
634 dupidx <- which(gnames == dupname) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
635 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
636 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
637 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
638 return (gnames) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
639 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
640 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
641 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
642 # https://github.com/sneumann/xcms/issues/247 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
643 .concatenate_XCMSnExp <- function(...) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
644 x <- list(...) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
645 if (length(x) == 0) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
646 return(NULL) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
647 if (length(x) == 1) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
648 return(x[[1]]) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
649 ## Check that all are XCMSnExp objects. |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
650 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp"))))) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
651 stop("All passed objects should be 'XCMSnExp' objects") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
652 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
653 ## If any of the XCMSnExp has alignment results or detected features drop |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
654 ## them! |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
655 x <- lapply(x, function(z) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
656 if (hasAdjustedRtime(z)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
657 z <- dropAdjustedRtime(z) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
658 warning("Adjusted retention times found, had to drop them.") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
659 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
660 if (hasFeatures(z)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
661 z <- dropFeatureDefinitions(z) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
662 warning("Feature definitions found, had to drop them.") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
663 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
664 z |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
665 }) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
666 ## Combine peaks |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
667 fls <- lapply(x, fileNames) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
668 startidx <- cumsum(lengths(fls)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
669 pks <- lapply(x, chromPeaks) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
670 procH <- lapply(x, processHistory) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
671 for (i in 2:length(fls)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
672 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
673 procH[[i]] <- lapply(procH[[i]], function(z) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
674 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1]) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
675 z |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
676 }) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
677 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
678 pks <- do.call(rbind, pks) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
679 new_x@.processHistory <- unlist(procH) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
diff
changeset
|
680 chromPeaks(new_x) <- pks |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
681 if (validObject(new_x)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
682 new_x |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
683 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
684 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
685 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
686 # https://github.com/sneumann/xcms/issues/247 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
687 .concatenate_OnDiskMSnExp <- function(...) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
688 x <- list(...) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
689 if (length(x) == 0) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
690 return(NULL) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
691 if (length(x) == 1) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
692 return(x[[1]]) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
693 ## Check that all are XCMSnExp objects. |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
694 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp"))))) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
695 stop("All passed objects should be 'OnDiskMSnExp' objects") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
696 ## Check processingQueue |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
697 procQ <- lapply(x, function(z) z@spectraProcessingQueue) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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parents:
diff
changeset
|
698 new_procQ <- procQ[[1]] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
699 is_ok <- unlist(lapply(procQ, function(z) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
700 !is.character(all.equal(new_procQ, z)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
701 )) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
702 if (any(!is_ok)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
703 warning("Processing queues from the submitted objects differ! ", |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
704 "Dropping the processing queue.") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
705 new_procQ <- list() |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
706 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
707 ## processingData |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
708 fls <- lapply(x, function(z) z@processingData@files) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
709 startidx <- cumsum(lengths(fls)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
710 ## featureData |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
711 featd <- lapply(x, fData) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
712 ## Have to update the file index and the spectrum names. |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
713 for (i in 2:length(featd)) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
714 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1] |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
715 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames( |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
716 fileIds = featd[[i]]$fileIdx, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
717 spectrumIds = featd[[i]]$spIdx, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
718 nSpectra = nrow(featd[[i]]), |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
719 nFiles = length(unlist(fls)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
720 ) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
721 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
722 featd <- do.call(rbind, featd) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
723 featd$spectrum <- 1:nrow(featd) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
724 ## experimentData |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
725 expdata <- lapply(x, function(z) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
726 ed <- z@experimentData |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
727 data.frame(instrumentManufacturer = ed@instrumentManufacturer, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
728 instrumentModel = ed@instrumentModel, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
729 ionSource = ed@ionSource, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
730 analyser = ed@analyser, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
731 detectorType = ed@detectorType, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
732 stringsAsFactors = FALSE) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
733 }) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
734 expdata <- do.call(rbind, expdata) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
735 expdata <- new("MIAPE", |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
736 instrumentManufacturer = expdata$instrumentManufacturer, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
737 instrumentModel = expdata$instrumentModel, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
738 ionSource = expdata$ionSource, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
739 analyser = expdata$analyser, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
740 detectorType = expdata$detectorType) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
741 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
742 ## protocolData |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
743 protodata <- lapply(x, function(z) z@protocolData) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
744 if (any(unlist(lapply(protodata, nrow)) > 0)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
745 warning("Found non-empty protocol data, but merging protocol data is", |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
746 " currently not supported. Skipped.") |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
747 ## phenoData |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
748 pdata <- do.call(rbind, lapply(x, pData)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
749 res <- new( |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
750 "OnDiskMSnExp", |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
751 phenoData = new("NAnnotatedDataFrame", data = pdata), |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
752 featureData = new("AnnotatedDataFrame", featd), |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
753 processingData = new("MSnProcess", |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
754 processing = paste0("Concatenated [", date(), "]"), |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
755 files = unlist(fls), smoothed = NA), |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
756 experimentData = expdata, |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
757 spectraProcessingQueue = new_procQ) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
758 if (validObject(res)) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
759 res |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
760 } |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
761 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
762 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
763 # https://github.com/sneumann/xcms/issues/247 |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
764 c.XCMSnExp <- function(...) { |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
765 .concatenate_XCMSnExp(...) |
dca722aecb67
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents:
diff
changeset
|
766 } |