xcms_summary: lib.r annotate

annotate lib.r @ 30:17562a6799a1 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f

author	lecorguille
date	Mon, 05 Mar 2018 04:18:38 -0500
parents	3d4339594010
children	0b5521b78c92

rev	line source
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	3
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	4 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	6 parseCommandArgs <- function(...) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	7 args <- batch::parseCommandArgs(...)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	8 for (key in names(args)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	9 if (args[key] %in% c("TRUE","FALSE"))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	10 args[key] = as.logical(args[key])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	11 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	12 return(args)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	13 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	14
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	15 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	16 # This function will
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	17 # - load the packages
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	18 # - display the sessionInfo
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	21
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	22 sessioninfo = sessionInfo()
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	23 cat(sessioninfo$R.version$version.string,"\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	24 cat("Main packages:\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	26 cat("Other loaded packages:\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	28 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	29
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	30 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	31 # This function convert if it is required the Retention Time in minutes
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	32 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	33 if (convertRTMinute){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	34 #converting the retention times (seconds) into minutes
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	35 print("converting the retention times into minutes in the variableMetadata")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	36 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	37 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	38 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	39 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	40 return (variableMetadata)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	41 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	42
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	43 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	44 # This function format ions identifiers
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	45 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	46 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	47 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	48 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	49 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	50 return(variableMetadata)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	51 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	52
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	53 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	54 # Draw the plotChromPeakDensity 3 per page in a pdf file
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	55 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	56 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	57
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	58 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	59
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	60 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	61 names(group_colors) <- unique(xdata$sample_group)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	62
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	63 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	64 for (i in 1:nrow(featureDefinitions(xdata))) {
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	65 mzmin = featureDefinitions(xdata)[i,]$mzmin
17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	66 mzmax = featureDefinitions(xdata)[i,]$mzmax
17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	67 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	68 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	69 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	70
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	71 dev.off()
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	72 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	73
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	74 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	75 # Draw the plotChromPeakDensity 3 per page in a pdf file
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	76 getPlotAdjustedRtime <- function(xdata) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	77 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	78 # Color by group
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	79 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	80 names(group_colors) <- unique(xdata$sample_group)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	81 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	82 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	83 # Color by sample
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	84 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	85 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	86 dev.off()
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	87 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	88
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	89 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	90 # value: intensity values to be used into, maxo or intb
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	91 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	92 dataMatrix <- featureValues(xdata, method="medret", value=intval)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	93 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	94 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	95 variableMetadata <- featureDefinitions(xdata)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	96 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	97 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	98
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	99 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	100 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	101
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	102 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	103 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	104
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	105 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	106
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	107 #@author Y. Guitton
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	108 getBPC <- function(file,rtcor=NULL, ...) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	109 object <- xcmsRaw(file)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	110 sel <- profRange(object, ...)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	111 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	112 #plotChrom(xcmsRaw(file), base=T)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	113 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	114
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	115 #@author Y. Guitton
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	116 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	117 cat("Creating BIC pdf...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	118
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	119 if (is.null(xcmsSet)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	120 cat("Enter an xcmsSet \n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	121 stop()
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	122 } else {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	123 files <- filepaths(xcmsSet)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	124 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	125
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	126 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	127
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	128 classnames <- vector("list",length(phenoDataClass))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	129 for (i in 1:length(phenoDataClass)){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	130 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	131 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	132
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	133 N <- dim(phenoData(xcmsSet))[1]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	134
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	135 TIC <- vector("list",N)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	136
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	137
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	138 for (j in 1:N) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	139
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	140 TIC[[j]] <- getBPC(files[j])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	141 #good for raw
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	142 # seems strange for corrected
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	143 #errors if scanrange used in xcmsSetgeneration
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	144 if (!is.null(xcmsSet) && rt == "corrected")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	145 rtcor <- xcmsSet@rt$corrected[[j]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	146 else
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	147 rtcor <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	148
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	149 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	150 # TIC[[j]][,1]<-rtcor
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	151 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	152
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	153
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	154
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	155 pdf(pdfname,w=16,h=10)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	156 cols <- rainbow(N)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	157 lty <- 1:N
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	158 pch <- 1:N
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	159 #search for max x and max y in BPCs
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	160 xlim <- range(sapply(TIC, function(x) range(x[,1])))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	161 ylim <- range(sapply(TIC, function(x) range(x[,2])))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	162 ylim <- c(-ylim[2], ylim[2])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	163
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	164
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	165 ##plot start
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	166
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	167 if (length(phenoDataClass)>2){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	168 for (k in 1:(length(phenoDataClass)-1)){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	169 for (l in (k+1):length(phenoDataClass)){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	170 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	171 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	172 colvect <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	173 for (j in 1:length(classnames[[k]])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	174 tic <- TIC[[classnames[[k]][j]]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	175 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	176 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	177 colvect <- append(colvect,cols[classnames[[k]][j]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	178 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	179 for (j in 1:length(classnames[[l]])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	180 # i <- class2names[j]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	181 tic <- TIC[[classnames[[l]][j]]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	182 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	183 colvect <- append(colvect,cols[classnames[[l]][j]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	184 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	185 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	186 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	187 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	188 }#end if length >2
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	189
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	190 if (length(phenoDataClass)==2){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	191 k <- 1
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	192 l <- 2
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	193 colvect <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	194 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	195
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	196 for (j in 1:length(classnames[[k]])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	197
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	198 tic <- TIC[[classnames[[k]][j]]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	199 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	200 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	201 colvect<-append(colvect,cols[classnames[[k]][j]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	202 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	203 for (j in 1:length(classnames[[l]])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	204 # i <- class2names[j]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	205 tic <- TIC[[classnames[[l]][j]]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	206 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	207 colvect <- append(colvect,cols[classnames[[l]][j]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	208 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	209 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	210
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	211 }#end length ==2
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	212
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	213 #case where only one class
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	214 if (length(phenoDataClass)==1){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	215 k <- 1
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	216 ylim <- range(sapply(TIC, function(x) range(x[,2])))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	217 colvect <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	218 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="BPC")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	219
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	220 for (j in 1:length(classnames[[k]])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	221 tic <- TIC[[classnames[[k]][j]]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	222 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	223 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	224 colvect <- append(colvect,cols[classnames[[k]][j]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	225 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	226
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	227 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	228
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	229 }#end length ==1
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	230
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	231 dev.off() #pdf(pdfname,w=16,h=10)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	232
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	233 invisible(TIC)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	234 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	235
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	236
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	237
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	238 #@author Y. Guitton
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	239 getTIC <- function(file, rtcor=NULL) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	240 object <- xcmsRaw(file)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	241 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object, mzrange=range(object@env$mz))$intensity)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	242 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	243
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	244 #overlay TIC from all files in current folder or from xcmsSet, create pdf
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	245 #@author Y. Guitton
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	246 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf", rt=c("raw","corrected")) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	247 cat("Creating TIC pdf...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	248
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	249 if (is.null(xcmsSet)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	250 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	251 filepattern <- paste(paste("\\.", filepattern, "$", sep=""), collapse="\|")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	252 if (is.null(files))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	253 files <- getwd()
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	254 info <- file.info(files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	255 listed <- list.files(files[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	256 files <- c(files[!info$isdir], listed)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	257 } else {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	258 files <- filepaths(xcmsSet)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	259 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	260
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	261 phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	262 classnames <- vector("list",length(phenoDataClass))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	263 for (i in 1:length(phenoDataClass)){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	264 classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	265 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	266
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	267 N <- length(files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	268 TIC <- vector("list",N)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	269
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	270 for (i in 1:N) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	271 if (!is.null(xcmsSet) && rt == "corrected")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	272 rtcor <- xcmsSet@rt$corrected[[i]] else
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	273 rtcor <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	274 TIC[[i]] <- getTIC(files[i], rtcor=rtcor)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	275 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	276
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	277 pdf(pdfname, w=16, h=10)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	278 cols <- rainbow(N)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	279 lty <- 1:N
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	280 pch <- 1:N
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	281 #search for max x and max y in TICs
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	282 xlim <- range(sapply(TIC, function(x) range(x[,1])))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	283 ylim <- range(sapply(TIC, function(x) range(x[,2])))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	284 ylim <- c(-ylim[2], ylim[2])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	285
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	286
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	287 ##plot start
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	288 if (length(phenoDataClass)>2){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	289 for (k in 1:(length(phenoDataClass)-1)){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	290 for (l in (k+1):length(phenoDataClass)){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	291 #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" "))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	292 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	293 colvect <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	294 for (j in 1:length(classnames[[k]])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	295 tic <- TIC[[classnames[[k]][j]]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	296 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	297 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	298 colvect <- append(colvect,cols[classnames[[k]][j]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	299 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	300 for (j in 1:length(classnames[[l]])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	301 # i=class2names[j]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	302 tic <- TIC[[classnames[[l]][j]]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	303 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	304 colvect <- append(colvect,cols[classnames[[l]][j]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	305 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	306 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	307 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	308 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	309 }#end if length >2
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	310 if (length(phenoDataClass)==2){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	311 k <- 1
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	312 l <- 2
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	313
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	314 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	315 colvect <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	316 for (j in 1:length(classnames[[k]])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	317 tic <- TIC[[classnames[[k]][j]]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	318 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	319 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	320 colvect <- append(colvect,cols[classnames[[k]][j]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	321 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	322 for (j in 1:length(classnames[[l]])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	323 # i <- class2names[j]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	324 tic <- TIC[[classnames[[l]][j]]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	325 points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	326 colvect <- append(colvect,cols[classnames[[l]][j]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	327 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	328 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	329
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	330 }#end length ==2
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	331
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	332 #case where only one class
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	333 if (length(phenoDataClass)==1){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	334 k <- 1
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	335 ylim <- range(sapply(TIC, function(x) range(x[,2])))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	336
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	337 plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="TIC")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	338 colvect <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	339 for (j in 1:length(classnames[[k]])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	340 tic <- TIC[[classnames[[k]][j]]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	341 # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	342 points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	343 colvect <- append(colvect,cols[classnames[[k]][j]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	344 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	345
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	346 legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	347
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	348 }#end length ==1
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	349
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	350 dev.off() #pdf(pdfname,w=16,h=10)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	351
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	352 invisible(TIC)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	353 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	354
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	355
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	356
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	357 # Get the polarities from all the samples of a condition
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	358 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	359 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	360 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	361 cat("Creating the sampleMetadata file...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	362
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	363 #Create the sampleMetada dataframe
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	364 sampleMetadata <- xdata@phenoData@data
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	365 rownames(sampleMetadata) <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	366 colnames(sampleMetadata) <- c("sampleMetadata", "class")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	367
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	368 sampleNamesOrigin <- sampleMetadata$sampleMetadata
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	369 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	370
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	371 if (any(duplicated(sampleNamesMakeNames))) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	372 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	373 for (sampleName in sampleNamesOrigin) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	374 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	375 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	376 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	377 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	378
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	379 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	380 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	381 for (sampleName in sampleNamesOrigin) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	382 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	383 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	384 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	385
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	386 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	387
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	388
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	389 #For each sample file, the following actions are done
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	390 for (fileIdx in 1:length(fileNames(xdata))) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	391 #Check if the file is in the CDF format
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	392 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	393
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	394 # If the column isn't exist, with add one filled with NA
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	395 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	396
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	397 #Extract the polarity (a list of polarities)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	398 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	399 #Verify if all the scans have the same polarity
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	400 uniq_list <- unique(polarity)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	401 if (length(uniq_list)>1){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	402 polarity <- "mixed"
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	403 } else {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	404 polarity <- as.character(uniq_list)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	405 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	406
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	407 #Set the polarity attribute
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	408 sampleMetadata$polarity[fileIdx] <- polarity
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	409 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	410
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	411 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	412
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	413 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	414
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	415 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	416
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	417 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	418
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	419
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	420 # This function check if xcms will found all the files
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	421 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	422 checkFilesCompatibilityWithXcms <- function(directory) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	423 cat("Checking files filenames compatibilities with xmcs...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	424 # WHAT XCMS WILL FIND
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	425 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	426 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	427 info <- file.info(directory)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	428 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	429 files <- c(directory[!info$isdir], listed)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	430 files_abs <- file.path(getwd(), files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	431 exists <- file.exists(files_abs)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	432 files[exists] <- files_abs[exists]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	433 files[exists] <- sub("//","/",files[exists])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	434
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	435 # WHAT IS ON THE FILESYSTEM
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	436 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.' -not -path 'conda-env' -type f -name \"\""), intern=T)
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	437 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	438
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	439 # COMPARISON
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	440 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	441 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	442 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	443 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	444 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	445 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	446
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	447
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	448 #This function list the compatible files within the directory as xcms did
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	449 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	450 getMSFiles <- function (directory) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	451 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	452 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	453 info <- file.info(directory)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	454 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	455 files <- c(directory[!info$isdir], listed)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	456 exists <- file.exists(files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	457 files <- files[exists]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	458 return(files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	459 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	460
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	461 # This function check if XML contains special caracters. It also checks integrity and completness.
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	462 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	463 checkXmlStructure <- function (directory) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	464 cat("Checking XML structure...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	465
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	466 cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	467 capture <- system(cmd, intern=TRUE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	468
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	469 if (length(capture)>0){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	470 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	471 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	472 write(capture, stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	473 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	474 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	475
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	476 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	477
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	478
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	479 # This function check if XML contain special characters
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	480 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	481 deleteXmlBadCharacters<- function (directory) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	482 cat("Checking Non ASCII characters in the XML...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	483
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	484 processed <- F
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	485 l <- system( paste0("find '",directory, "' -not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'"), intern=TRUE)
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	486 for (i in l){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	487 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	488 capture <- suppressWarnings(system(cmd, intern=TRUE))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	489 if (length(capture)>0){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	490 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	491 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	492 c <- system(cmd, intern=TRUE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	493 capture <- ""
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	494 processed <- T
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	495 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	496 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	497 if (processed) cat("\n\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	498 return(processed)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	499 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	500
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	501
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	502 # This function will compute MD5 checksum to check the data integrity
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	503 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	504 getMd5sum <- function (directory) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	505 cat("Compute md5 checksum...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	506 # WHAT XCMS WILL FIND
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	507 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	508 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	509 info <- file.info(directory)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	510 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	511 files <- c(directory[!info$isdir], listed)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	512 exists <- file.exists(files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	513 files <- files[exists]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	514
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	515 library(tools)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	516
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	517 #cat("\n\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	518
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	519 return(as.matrix(md5sum(files)))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	520 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	521
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	522
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	523 # This function get the raw file path from the arguments
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	524 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	525 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	526 if (!is.null(args$zipfile)) zipfile <- args$zipfile
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	527 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	528 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	529
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	530 if (!is.null(args$singlefile_galaxyPath)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	531 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	532 singlefile_sampleNames <- args$singlefile_sampleName
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	533 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	534 if (!is.null(args$singlefile_galaxyPathPositive)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	535 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	536 singlefile_sampleNames <- args$singlefile_sampleNamePositive
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	537 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	538 if (!is.null(args$singlefile_galaxyPathNegative)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	539 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	540 singlefile_sampleNames <- args$singlefile_sampleNameNegative
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	541 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	542 if (exists("singlefile_galaxyPaths")){
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	543 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\\|"))
17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	544 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\\|"))
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	545
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	546 singlefile <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	547 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	548 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	549 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	550 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	551 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	552 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	553 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	554 args[[argument]] <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	555 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	556 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	557 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	558
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	559
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	560 # This function retrieve the raw file in the working directory
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	561 # - if zipfile: unzip the file with its directory tree
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	562 # - if singlefiles: set symlink with the good filename
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	563 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	564 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	565 if(!is.null(singlefile) && (length("singlefile")>0)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	566 for (singlefile_sampleName in names(singlefile)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	567 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	568 if(!file.exists(singlefile_galaxyPath)){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	569 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	570 print(error_message); stop(error_message)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	571 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	572
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	573 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	574 file.copy(singlefile_galaxyPath, singlefile_sampleName)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	575
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	576 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	577 directory <- "."
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	578
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	579 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	580 if(!is.null(zipfile) && (zipfile != "")) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	581 if(!file.exists(zipfile)){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	582 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	583 print(error_message)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	584 stop(error_message)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	585 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	586
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	587 #list all file in the zip file
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	588 #zip_files <- unzip(zipfile,list=T)[,"Name"]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	589
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	590 #unzip
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	591 suppressWarnings(unzip(zipfile, unzip="unzip"))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	592
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	593 #get the directory name
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	594 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	595 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	596 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	597 directory <- "."
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	598 if (length(directories) == 1) directory <- directories
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	599
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	600 cat("files_root_directory\t",directory,"\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	601
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	602 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	603 return (directory)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	604 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	605
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	606
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	607 # This function retrieve a xset like object
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	608 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	609 getxcmsSetObject <- function(xobject) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	610 # XCMS 1.x
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	611 if (class(xobject) == "xcmsSet")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	612 return (xobject)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	613 # XCMS 3.x
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	614 if (class(xobject) == "XCMSnExp") {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	615 # Get the legacy xcmsSet object
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	616 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	617 sampclass(xset) <- xset@phenoData$sample_group
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	618 return (xset)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	619 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	620 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	621
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	622
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	623 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	624 # https://github.com/sneumann/xcms/issues/250
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	625 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	626 mzfmt <- paste("%.", mzdec, "f", sep = "")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	627 rtfmt <- paste("%.", rtdec, "f", sep = "")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	628
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	629 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	630 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	631
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	632 if (any(dup <- duplicated(gnames)))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	633 for (dupname in unique(gnames[dup])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	634 dupidx <- which(gnames == dupname)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	635 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	636 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	637
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	638 return (gnames)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	639 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	640
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	641 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	642 # https://github.com/sneumann/xcms/issues/247
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	643 .concatenate_XCMSnExp <- function(...) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	644 x <- list(...)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	645 if (length(x) == 0)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	646 return(NULL)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	647 if (length(x) == 1)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	648 return(x[[1]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	649 ## Check that all are XCMSnExp objects.
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	650 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	651 stop("All passed objects should be 'XCMSnExp' objects")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	652 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	653 ## If any of the XCMSnExp has alignment results or detected features drop
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	654 ## them!
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	655 x <- lapply(x, function(z) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	656 if (hasAdjustedRtime(z)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	657 z <- dropAdjustedRtime(z)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	658 warning("Adjusted retention times found, had to drop them.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	659 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	660 if (hasFeatures(z)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	661 z <- dropFeatureDefinitions(z)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	662 warning("Feature definitions found, had to drop them.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	663 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	664 z
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	665 })
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	666 ## Combine peaks
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	667 fls <- lapply(x, fileNames)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	668 startidx <- cumsum(lengths(fls))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	669 pks <- lapply(x, chromPeaks)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	670 procH <- lapply(x, processHistory)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	671 for (i in 2:length(fls)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	672 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	673 procH[[i]] <- lapply(procH[[i]], function(z) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	674 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	675 z
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	676 })
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	677 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	678 pks <- do.call(rbind, pks)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	679 new_x@.processHistory <- unlist(procH)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	680 chromPeaks(new_x) <- pks
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	681 if (validObject(new_x))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	682 new_x
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	683 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	684
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	685 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	686 # https://github.com/sneumann/xcms/issues/247
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	687 .concatenate_OnDiskMSnExp <- function(...) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	688 x <- list(...)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	689 if (length(x) == 0)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	690 return(NULL)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	691 if (length(x) == 1)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	692 return(x[[1]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	693 ## Check that all are XCMSnExp objects.
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	694 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	695 stop("All passed objects should be 'OnDiskMSnExp' objects")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	696 ## Check processingQueue
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	697 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	698 new_procQ <- procQ[[1]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	699 is_ok <- unlist(lapply(procQ, function(z)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	700 !is.character(all.equal(new_procQ, z))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	701 ))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	702 if (any(!is_ok)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	703 warning("Processing queues from the submitted objects differ! ",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	704 "Dropping the processing queue.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	705 new_procQ <- list()
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	706 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	707 ## processingData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	708 fls <- lapply(x, function(z) z@processingData@files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	709 startidx <- cumsum(lengths(fls))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	710 ## featureData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	711 featd <- lapply(x, fData)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	712 ## Have to update the file index and the spectrum names.
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	713 for (i in 2:length(featd)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	714 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	715 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	716 fileIds = featd[[i]]$fileIdx,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	717 spectrumIds = featd[[i]]$spIdx,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	718 nSpectra = nrow(featd[[i]]),
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	719 nFiles = length(unlist(fls))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	720 )
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	721 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	722 featd <- do.call(rbind, featd)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	723 featd$spectrum <- 1:nrow(featd)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	724 ## experimentData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	725 expdata <- lapply(x, function(z) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	726 ed <- z@experimentData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	727 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	728 instrumentModel = ed@instrumentModel,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	729 ionSource = ed@ionSource,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	730 analyser = ed@analyser,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	731 detectorType = ed@detectorType,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	732 stringsAsFactors = FALSE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	733 })
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	734 expdata <- do.call(rbind, expdata)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	735 expdata <- new("MIAPE",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	736 instrumentManufacturer = expdata$instrumentManufacturer,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	737 instrumentModel = expdata$instrumentModel,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	738 ionSource = expdata$ionSource,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	739 analyser = expdata$analyser,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	740 detectorType = expdata$detectorType)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	741
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	742 ## protocolData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	743 protodata <- lapply(x, function(z) z@protocolData)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	744 if (any(unlist(lapply(protodata, nrow)) > 0))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	745 warning("Found non-empty protocol data, but merging protocol data is",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	746 " currently not supported. Skipped.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	747 ## phenoData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	748 pdata <- do.call(rbind, lapply(x, pData))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	749 res <- new(
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	750 "OnDiskMSnExp",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	751 phenoData = new("NAnnotatedDataFrame", data = pdata),
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	752 featureData = new("AnnotatedDataFrame", featd),
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	753 processingData = new("MSnProcess",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	754 processing = paste0("Concatenated [", date(), "]"),
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	755 files = unlist(fls), smoothed = NA),
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	756 experimentData = expdata,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	757 spectraProcessingQueue = new_procQ)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	758 if (validObject(res))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	759 res
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	760 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	761
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	762 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	763 # https://github.com/sneumann/xcms/issues/247
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	764 c.XCMSnExp <- function(...) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	765 .concatenate_XCMSnExp(...)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	766 }

Mercurial > repos > lecorguille > xcms_summary

annotate lib.r @ 30:17562a6799a1 draft