xcms_xcmsset: lib.r annotate

annotate lib.r @ 32:2bf1cb023c94 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e

author	lecorguille
date	Thu, 01 Mar 2018 04:14:39 -0500
parents	e93153c07be0
children	c363b9f1caef

rev	line source
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	3
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	4 #@author G. Le Corguille
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	6 parseCommandArgs <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	7 args <- batch::parseCommandArgs(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	8 for (key in names(args)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	9 if (args[key] %in% c("TRUE","FALSE"))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	10 args[key] = as.logical(args[key])
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	11 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	12 return(args)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	13 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	14
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	15 #@author G. Le Corguille
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	16 # This function will
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	17 # - load the packages
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	18 # - display the sessionInfo
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	21
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	22 sessioninfo = sessionInfo()
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	23 cat(sessioninfo$R.version$version.string,"\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	24 cat("Main packages:\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	26 cat("Other loaded packages:\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	28 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	29
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	30 #@author G. Le Corguille
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	31 # This function convert if it is required the Retention Time in minutes
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	32 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	33 if (convertRTMinute){
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	34 #converting the retention times (seconds) into minutes
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	35 print("converting the retention times into minutes in the variableMetadata")
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	36 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	37 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	38 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	39 }
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	40 return (variableMetadata)
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	41 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	42
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	43 #@author G. Le Corguille
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	44 # This function format ions identifiers
21 ab238b104c3f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 20 diff changeset	45 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	46 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	47 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	48 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	49 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
21 ab238b104c3f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 20 diff changeset	50 return(variableMetadata)
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	51 }
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	52
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	53 #@author G. Le Corguille
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	54 # Draw the plotChromPeakDensity 3 per page in a pdf file
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	55 getPlotChromPeakDensity <- function(xdata) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	56 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	57
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	58 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	59
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	60 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	61 names(group_colors) <- unique(xdata$sample_group)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	62
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	63 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	64 for (i in 1:nrow(featureDefinitions(xdata))) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	65 plotChromPeakDensity(xdata, mz=c(featureDefinitions(xdata)[i,]$mzmin,featureDefinitions(xdata)[i,]$mzmax), col=group_colors, pch=16, xlim=xlim)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	66 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	67 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	68
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	69 dev.off()
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	70 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	71
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	72 #@author G. Le Corguille
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	73 # Draw the plotChromPeakDensity 3 per page in a pdf file
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	74 getPlotAdjustedRtime <- function(xdata) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	75 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	76 # Color by group
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	77 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	78 names(group_colors) <- unique(xdata$sample_group)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	79 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	80 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	81 # Color by sample
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	82 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	83 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	84 dev.off()
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	85 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	86
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	87 #@author G. Le Corguille
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	88 # value: intensity values to be used into, maxo or intb
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	89 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	90 dataMatrix <- featureValues(xdata, method="medret", value=intval)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	91 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	92 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	93 variableMetadata <- featureDefinitions(xdata)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	94 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	95 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	96
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	97 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	98 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	99
21 ab238b104c3f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 20 diff changeset	100 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
ab238b104c3f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 20 diff changeset	101 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	102
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	103 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	104
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	105 #@author Y. Guitton
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	106 getBPC <- function(file,rtcor=NULL, ...) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	107 object <- xcmsRaw(file)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	108 sel <- profRange(object, ...)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	109 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	110 #plotChrom(xcmsRaw(file), base=T)
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	111 }
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	112
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	113 #@author Y. Guitton
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	114 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	115 cat("Creating BIC pdf...\n")
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	116
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	117 if (is.null(xcmsSet)) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	118 cat("Enter an xcmsSet \n")
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	119 stop()
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	120 } else {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	121 files <- filepaths(xcmsSet)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	122 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	123
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	124 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	125
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	126 classnames <- vector("list",length(phenoDataClass))
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	127 for (i in 1:length(phenoDataClass)){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	128 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	129 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	130
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	131 N <- dim(phenoData(xcmsSet))[1]
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	132
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	133 TIC <- vector("list",N)
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	134
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	135
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	136 for (j in 1:N) {
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	137
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	138 TIC[[j]] <- getBPC(files[j])
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	139 #good for raw
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	140 # seems strange for corrected
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	141 #errors if scanrange used in xcmsSetgeneration
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	142 if (!is.null(xcmsSet) && rt == "corrected")
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	143 rtcor <- xcmsSet@rt$corrected[[j]]
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	144 else
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	145 rtcor <- NULL
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	146
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	147 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	148 # TIC[[j]][,1]<-rtcor
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	149 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	150
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	151
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	152
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	153 pdf(pdfname,w=16,h=10)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	154 cols <- rainbow(N)
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	155 lty <- 1:N
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	156 pch <- 1:N
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	157 #search for max x and max y in BPCs
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	158 xlim <- range(sapply(TIC, function(x) range(x[,1])))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	159 ylim <- range(sapply(TIC, function(x) range(x[,2])))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	160 ylim <- c(-ylim[2], ylim[2])
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	161
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	162
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	163 ##plot start
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	164
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	165 if (length(phenoDataClass)>2){
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	166 for (k in 1:(length(phenoDataClass)-1)){
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	167 for (l in (k+1):length(phenoDataClass)){
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	168 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	169 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")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	170 colvect <- NULL
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	171 for (j in 1:length(classnames[[k]])) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	172 tic <- TIC[[classnames[[k]][j]]]
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	173 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	174 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	175 colvect <- append(colvect,cols[classnames[[k]][j]])
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	176 }
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	177 for (j in 1:length(classnames[[l]])) {
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	178 # i <- class2names[j]
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	179 tic <- TIC[[classnames[[l]][j]]]
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	180 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	181 colvect <- append(colvect,cols[classnames[[l]][j]])
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	182 }
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	183 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	184 }
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	185 }
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	186 }#end if length >2
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	187
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	188 if (length(phenoDataClass)==2){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	189 k <- 1
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	190 l <- 2
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	191 colvect <- NULL
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	192 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")
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	193
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	194 for (j in 1:length(classnames[[k]])) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	195
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	196 tic <- TIC[[classnames[[k]][j]]]
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	197 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	198 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	199 colvect<-append(colvect,cols[classnames[[k]][j]])
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	200 }
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	201 for (j in 1:length(classnames[[l]])) {
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	202 # i <- class2names[j]
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	203 tic <- TIC[[classnames[[l]][j]]]
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	204 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	205 colvect <- append(colvect,cols[classnames[[l]][j]])
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	206 }
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	207 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	208
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	209 }#end length ==2
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	210
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	211 #case where only one class
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	212 if (length(phenoDataClass)==1){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	213 k <- 1
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	214 ylim <- range(sapply(TIC, function(x) range(x[,2])))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	215 colvect <- NULL
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	216 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")
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	217
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	218 for (j in 1:length(classnames[[k]])) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	219 tic <- TIC[[classnames[[k]][j]]]
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	220 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	221 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	222 colvect <- append(colvect,cols[classnames[[k]][j]])
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	223 }
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	224
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	225 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	226
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	227 }#end length ==1
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	228
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	229 dev.off() #pdf(pdfname,w=16,h=10)
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	230
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	231 invisible(TIC)
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	232 }
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	233
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	234
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	235
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	236 #@author Y. Guitton
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	237 getTIC <- function(file, rtcor=NULL) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	238 object <- xcmsRaw(file)
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	239 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object, mzrange=range(object@env$mz))$intensity)
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	240 }
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	241
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	242 #overlay TIC from all files in current folder or from xcmsSet, create pdf
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	243 #@author Y. Guitton
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	244 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf", rt=c("raw","corrected")) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	245 cat("Creating TIC pdf...\n")
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	246
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	247 if (is.null(xcmsSet)) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	248 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	249 filepattern <- paste(paste("\\.", filepattern, "$", sep=""), collapse="\|")
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	250 if (is.null(files))
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	251 files <- getwd()
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	252 info <- file.info(files)
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	253 listed <- list.files(files[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	254 files <- c(files[!info$isdir], listed)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	255 } else {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	256 files <- filepaths(xcmsSet)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	257 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	258
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	259 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	260 classnames <- vector("list",length(phenoDataClass))
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	261 for (i in 1:length(phenoDataClass)){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	262 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	263 }
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	264
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	265 N <- length(files)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	266 TIC <- vector("list",N)
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	267
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	268 for (i in 1:N) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	269 if (!is.null(xcmsSet) && rt == "corrected")
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	270 rtcor <- xcmsSet@rt$corrected[[i]] else
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	271 rtcor <- NULL
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	272 TIC[[i]] <- getTIC(files[i], rtcor=rtcor)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	273 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	274
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	275 pdf(pdfname, w=16, h=10)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	276 cols <- rainbow(N)
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	277 lty <- 1:N
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	278 pch <- 1:N
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	279 #search for max x and max y in TICs
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	280 xlim <- range(sapply(TIC, function(x) range(x[,1])))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	281 ylim <- range(sapply(TIC, function(x) range(x[,2])))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	282 ylim <- c(-ylim[2], ylim[2])
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	283
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	284
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	285 ##plot start
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	286 if (length(phenoDataClass)>2){
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	287 for (k in 1:(length(phenoDataClass)-1)){
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	288 for (l in (k+1):length(phenoDataClass)){
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	289 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	290 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")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	291 colvect <- NULL
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	292 for (j in 1:length(classnames[[k]])) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	293 tic <- TIC[[classnames[[k]][j]]]
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	294 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	295 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	296 colvect <- append(colvect,cols[classnames[[k]][j]])
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	297 }
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	298 for (j in 1:length(classnames[[l]])) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	299 # i=class2names[j]
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	300 tic <- TIC[[classnames[[l]][j]]]
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	301 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	302 colvect <- append(colvect,cols[classnames[[l]][j]])
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	303 }
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	304 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	305 }
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	306 }
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	307 }#end if length >2
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	308 if (length(phenoDataClass)==2){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	309 k <- 1
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	310 l <- 2
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	311
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	312 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")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	313 colvect <- NULL
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	314 for (j in 1:length(classnames[[k]])) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	315 tic <- TIC[[classnames[[k]][j]]]
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	316 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	317 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	318 colvect <- append(colvect,cols[classnames[[k]][j]])
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	319 }
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	320 for (j in 1:length(classnames[[l]])) {
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	321 # i <- class2names[j]
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	322 tic <- TIC[[classnames[[l]][j]]]
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	323 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	324 colvect <- append(colvect,cols[classnames[[l]][j]])
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	325 }
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	326 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	327
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	328 }#end length ==2
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	329
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	330 #case where only one class
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	331 if (length(phenoDataClass)==1){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	332 k <- 1
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	333 ylim <- range(sapply(TIC, function(x) range(x[,2])))
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	334
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	335 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")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	336 colvect <- NULL
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	337 for (j in 1:length(classnames[[k]])) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	338 tic <- TIC[[classnames[[k]][j]]]
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	339 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	340 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	341 colvect <- append(colvect,cols[classnames[[k]][j]])
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	342 }
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	343
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	344 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	345
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	346 }#end length ==1
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	347
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	348 dev.off() #pdf(pdfname,w=16,h=10)
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	349
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	350 invisible(TIC)
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	351 }
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	352
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	353
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	354
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	355 # Get the polarities from all the samples of a condition
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	356 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	357 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	358 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	359 cat("Creating the sampleMetadata file...\n")
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	360
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	361 #Create the sampleMetada dataframe
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	362 sampleMetadata <- xdata@phenoData@data
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	363 rownames(sampleMetadata) <- NULL
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	364 colnames(sampleMetadata) <- c("sampleMetadata", "class")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	365
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	366 sampleNamesOrigin <- sampleMetadata$sampleMetadata
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	367 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	368
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	369 if (any(duplicated(sampleNamesMakeNames))) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	370 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())
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	371 for (sampleName in sampleNamesOrigin) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	372 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	373 }
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	374 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	375 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	376
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	377 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	378 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")
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	379 for (sampleName in sampleNamesOrigin) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	380 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	381 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	382 }
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	383
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	384 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	385
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	386
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	387 #For each sample file, the following actions are done
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	388 for (fileIdx in 1:length(fileNames(xdata))) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	389 #Check if the file is in the CDF format
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	390 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	391
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	392 # If the column isn't exist, with add one filled with NA
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	393 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	394
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	395 #Extract the polarity (a list of polarities)
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	396 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	397 #Verify if all the scans have the same polarity
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	398 uniq_list <- unique(polarity)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	399 if (length(uniq_list)>1){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	400 polarity <- "mixed"
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	401 } else {
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	402 polarity <- as.character(uniq_list)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	403 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	404
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	405 #Set the polarity attribute
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	406 sampleMetadata$polarity[fileIdx] <- polarity
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	407 }
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	408
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	409 }
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	410
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	411 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	412
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	413 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	414
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	415 }
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	416
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	417
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	418 # This function check if xcms will found all the files
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	419 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	420 checkFilesCompatibilityWithXcms <- function(directory) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	421 cat("Checking files filenames compatibilities with xmcs...\n")
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	422 # WHAT XCMS WILL FIND
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	423 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	424 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	425 info <- file.info(directory)
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	426 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	427 files <- c(directory[!info$isdir], listed)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	428 files_abs <- file.path(getwd(), files)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	429 exists <- file.exists(files_abs)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	430 files[exists] <- files_abs[exists]
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	431 files[exists] <- sub("//","/",files[exists])
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	432
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	433 # WHAT IS ON THE FILESYSTEM
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	434 filesystem_filepaths <- system(paste("find $PWD/",directory," -not -name '\\.' -not -path 'conda-env' -type f -name \"\"", sep=""), intern=T)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	435 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	436
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	437 # COMPARISON
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	438 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	439 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	440 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	441 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	442 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	443 }
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	444
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	445
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	446 #This function list the compatible files within the directory as xcms did
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	447 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	448 getMSFiles <- function (directory) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	449 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	450 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	451 info <- file.info(directory)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	452 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	453 files <- c(directory[!info$isdir], listed)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	454 exists <- file.exists(files)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	455 files <- files[exists]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	456 return(files)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	457 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	458
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	459 # This function check if XML contains special caracters. It also checks integrity and completness.
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	460 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	461 checkXmlStructure <- function (directory) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	462 cat("Checking XML structure...\n")
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	463
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	464 cmd <- paste("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;")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	465 capture <- system(cmd, intern=TRUE)
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	466
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	467 if (length(capture)>0){
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	468 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	469 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	470 write(capture, stderr())
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	471 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	472 }
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	473
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	474 }
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	475
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	476
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	477 # This function check if XML contain special characters
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	478 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	479 deleteXmlBadCharacters<- function (directory) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	480 cat("Checking Non ASCII characters in the XML...\n")
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	481
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	482 processed <- F
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	483 l <- system( paste("find",directory, "-not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'"), intern=TRUE)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	484 for (i in l){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	485 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	486 capture <- suppressWarnings(system(cmd, intern=TRUE))
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	487 if (length(capture)>0){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	488 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	489 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	490 c <- system(cmd, intern=TRUE)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	491 capture <- ""
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	492 processed <- T
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	493 }
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	494 }
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	495 if (processed) cat("\n\n")
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	496 return(processed)
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	497 }
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	498
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	499
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	500 # This function will compute MD5 checksum to check the data integrity
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	501 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	502 getMd5sum <- function (directory) {
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	503 cat("Compute md5 checksum...\n")
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	504 # WHAT XCMS WILL FIND
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	505 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	506 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	507 info <- file.info(directory)
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	508 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	509 files <- c(directory[!info$isdir], listed)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	510 exists <- file.exists(files)
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	511 files <- files[exists]
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	512
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	513 library(tools)
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	514
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	515 #cat("\n\n")
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	516
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	517 return(as.matrix(md5sum(files)))
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: diff changeset	518 }
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	519
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	520
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	521 # This function get the raw file path from the arguments
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	522 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	523 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	524 if (!is.null(args$zipfile)) zipfile <- args$zipfile
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	525 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	526 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	527
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	528 if (!is.null(args$singlefile_galaxyPath)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	529 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	530 singlefile_sampleNames <- args$singlefile_sampleName
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	531 }
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	532 if (!is.null(args$singlefile_galaxyPathPositive)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	533 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	534 singlefile_sampleNames <- args$singlefile_sampleNamePositive
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	535 }
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	536 if (!is.null(args$singlefile_galaxyPathNegative)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	537 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	538 singlefile_sampleNames <- args$singlefile_sampleNameNegative
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	539 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	540 if (exists("singlefile_galaxyPaths")){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	541 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,","))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	542 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,","))
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	543
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	544 singlefile <- NULL
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	545 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	546 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	547 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	548 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	549 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	550 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	551 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	552 args[[argument]] <- NULL
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	553 }
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	554 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	555 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	556
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	557
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	558 # This function retrieve the raw file in the working directory
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	559 # - if zipfile: unzip the file with its directory tree
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	560 # - if singlefiles: set symlink with the good filename
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	561 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	562 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	563 if(!is.null(singlefile) && (length("singlefile")>0)) {
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	564 for (singlefile_sampleName in names(singlefile)) {
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	565 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	566 if(!file.exists(singlefile_galaxyPath)){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	567 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	568 print(error_message); stop(error_message)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	569 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	570
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	571 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	572 file.copy(singlefile_galaxyPath, singlefile_sampleName)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	573
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	574 }
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	575 directory <- "."
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	576
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	577 }
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	578 if(!is.null(zipfile) && (zipfile != "")) {
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	579 if(!file.exists(zipfile)){
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	580 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	581 print(error_message)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	582 stop(error_message)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	583 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	584
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	585 #list all file in the zip file
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	586 #zip_files <- unzip(zipfile,list=T)[,"Name"]
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	587
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	588 #unzip
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	589 suppressWarnings(unzip(zipfile, unzip="unzip"))
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	590
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	591 #get the directory name
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	592 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	593 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	594 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	595 directory <- "."
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	596 if (length(directories) == 1) directory <- directories
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	597
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	598 cat("files_root_directory\t",directory,"\n")
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	599
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	600 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	601 return (directory)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 21 diff changeset	602 }
32 2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	603
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	604
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	605 # This function retrieve a xset like object
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	606 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	607 getxcmsSetObject <- function(xobject) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	608 # XCMS 1.x
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	609 if (class(xobject) == "xcmsSet")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	610 return (xobject)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	611 # XCMS 3.x
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	612 if (class(xobject) == "XCMSnExp") {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	613 # Get the legacy xcmsSet object
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	614 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	615 sampclass(xset) <- xset@phenoData$sample_group
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	616 return (xset)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	617 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	618 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	619
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	620
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	621 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	622 # https://github.com/sneumann/xcms/issues/250
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	623 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	624 mzfmt <- paste("%.", mzdec, "f", sep = "")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	625 rtfmt <- paste("%.", rtdec, "f", sep = "")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	626
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	627 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	628 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	629
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	630 if (any(dup <- duplicated(gnames)))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	631 for (dupname in unique(gnames[dup])) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	632 dupidx <- which(gnames == dupname)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	633 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	634 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	635
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	636 return (gnames)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	637 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	638
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	639 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	640 # https://github.com/sneumann/xcms/issues/247
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	641 .concatenate_XCMSnExp <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	642 x <- list(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	643 if (length(x) == 0)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	644 return(NULL)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	645 if (length(x) == 1)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	646 return(x[[1]])
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	647 ## Check that all are XCMSnExp objects.
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	648 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	649 stop("All passed objects should be 'XCMSnExp' objects")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	650 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	651 ## If any of the XCMSnExp has alignment results or detected features drop
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	652 ## them!
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	653 x <- lapply(x, function(z) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	654 if (hasAdjustedRtime(z)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	655 z <- dropAdjustedRtime(z)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	656 warning("Adjusted retention times found, had to drop them.")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	657 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	658 if (hasFeatures(z)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	659 z <- dropFeatureDefinitions(z)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	660 warning("Feature definitions found, had to drop them.")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	661 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	662 z
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	663 })
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	664 ## Combine peaks
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	665 fls <- lapply(x, fileNames)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	666 startidx <- cumsum(lengths(fls))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	667 pks <- lapply(x, chromPeaks)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	668 procH <- lapply(x, processHistory)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	669 for (i in 2:length(fls)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	670 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	671 procH[[i]] <- lapply(procH[[i]], function(z) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	672 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	673 z
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	674 })
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	675 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	676 pks <- do.call(rbind, pks)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	677 new_x@.processHistory <- unlist(procH)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	678 chromPeaks(new_x) <- pks
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	679 if (validObject(new_x))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	680 new_x
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	681 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	682
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	683 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	684 # https://github.com/sneumann/xcms/issues/247
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	685 .concatenate_OnDiskMSnExp <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	686 x <- list(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	687 if (length(x) == 0)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	688 return(NULL)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	689 if (length(x) == 1)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	690 return(x[[1]])
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	691 ## Check that all are XCMSnExp objects.
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	692 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	693 stop("All passed objects should be 'OnDiskMSnExp' objects")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	694 ## Check processingQueue
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	695 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	696 new_procQ <- procQ[[1]]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	697 is_ok <- unlist(lapply(procQ, function(z)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	698 !is.character(all.equal(new_procQ, z))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	699 ))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	700 if (any(!is_ok)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	701 warning("Processing queues from the submitted objects differ! ",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	702 "Dropping the processing queue.")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	703 new_procQ <- list()
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	704 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	705 ## processingData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	706 fls <- lapply(x, function(z) z@processingData@files)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	707 startidx <- cumsum(lengths(fls))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	708 ## featureData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	709 featd <- lapply(x, fData)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	710 ## Have to update the file index and the spectrum names.
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	711 for (i in 2:length(featd)) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	712 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	713 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	714 fileIds = featd[[i]]$fileIdx,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	715 spectrumIds = featd[[i]]$spIdx,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	716 nSpectra = nrow(featd[[i]]),
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	717 nFiles = length(unlist(fls))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	718 )
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	719 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	720 featd <- do.call(rbind, featd)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	721 featd$spectrum <- 1:nrow(featd)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	722 ## experimentData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	723 expdata <- lapply(x, function(z) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	724 ed <- z@experimentData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	725 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	726 instrumentModel = ed@instrumentModel,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	727 ionSource = ed@ionSource,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	728 analyser = ed@analyser,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	729 detectorType = ed@detectorType,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	730 stringsAsFactors = FALSE)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	731 })
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	732 expdata <- do.call(rbind, expdata)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	733 expdata <- new("MIAPE",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	734 instrumentManufacturer = expdata$instrumentManufacturer,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	735 instrumentModel = expdata$instrumentModel,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	736 ionSource = expdata$ionSource,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	737 analyser = expdata$analyser,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	738 detectorType = expdata$detectorType)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	739
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	740 ## protocolData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	741 protodata <- lapply(x, function(z) z@protocolData)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	742 if (any(unlist(lapply(protodata, nrow)) > 0))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	743 warning("Found non-empty protocol data, but merging protocol data is",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	744 " currently not supported. Skipped.")
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	745 ## phenoData
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	746 pdata <- do.call(rbind, lapply(x, pData))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	747 res <- new(
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	748 "OnDiskMSnExp",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	749 phenoData = new("NAnnotatedDataFrame", data = pdata),
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	750 featureData = new("AnnotatedDataFrame", featd),
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	751 processingData = new("MSnProcess",
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	752 processing = paste0("Concatenated [", date(), "]"),
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	753 files = unlist(fls), smoothed = NA),
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	754 experimentData = expdata,
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	755 spectraProcessingQueue = new_procQ)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	756 if (validObject(res))
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	757 res
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	758 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	759
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	760 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	761 # https://github.com/sneumann/xcms/issues/247
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	762 c.XCMSnExp <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	763 .concatenate_XCMSnExp(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 31 diff changeset	764 }

Mercurial > repos > lecorguille > xcms_xcmsset

annotate lib.r @ 32:2bf1cb023c94 draft