xcms_plot_chromatogram: lib.r annotate

annotate lib.r @ 1:86ff4497b871 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309

author	lecorguille
date	Thu, 08 Mar 2018 05:52:12 -0500
parents	fe1f0f16d9e6
children	e6fdadaf039e

rev	line source
0 fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	3
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	4 #@author G. Le Corguille
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	6 parseCommandArgs <- function(...) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	7 args <- batch::parseCommandArgs(...)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	8 for (key in names(args)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	9 if (args[key] %in% c("TRUE","FALSE"))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	10 args[key] = as.logical(args[key])
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	11 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	12 return(args)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	13 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	14
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	15 #@author G. Le Corguille
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	16 # This function will
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	17 # - load the packages
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	18 # - display the sessionInfo
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	21
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	22 sessioninfo = sessionInfo()
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	23 cat(sessioninfo$R.version$version.string,"\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	24 cat("Main packages:\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	26 cat("Other loaded packages:\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	28 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	29
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	30 #@author G. Le Corguille
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	31 # This function convert if it is required the Retention Time in minutes
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	32 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	33 if (convertRTMinute){
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	34 #converting the retention times (seconds) into minutes
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	35 print("converting the retention times into minutes in the variableMetadata")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	36 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	37 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	38 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	39 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	40 return (variableMetadata)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	41 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	42
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	43 #@author G. Le Corguille
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	44 # This function format ions identifiers
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	45 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	46 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	47 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	48 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	49 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	50 return(variableMetadata)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	51 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	52
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	53 #@author G. Le Corguille
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	54 # Draw the plotChromPeakDensity 3 per page in a pdf file
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	55 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	56 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	57
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	58 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	59
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	60 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	61 names(group_colors) <- unique(xdata$sample_group)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	62
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	63 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	64 for (i in 1:nrow(featureDefinitions(xdata))) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	65 mzmin = featureDefinitions(xdata)[i,]$mzmin
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	66 mzmax = featureDefinitions(xdata)[i,]$mzmax
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	67 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	68 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	69 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	70
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	71 dev.off()
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	72 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	73
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	74 #@author G. Le Corguille
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	75 # Draw the plotChromPeakDensity 3 per page in a pdf file
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	76 getPlotAdjustedRtime <- function(xdata) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	77
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	78 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	79
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	80 # Color by group
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	81 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	82 names(group_colors) <- unique(xdata$sample_group)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	83 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	84 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	85
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	86 # Color by sample
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	87 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	88 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	89
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	90 dev.off()
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	91 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	92
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	93 #@author G. Le Corguille
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	94 # value: intensity values to be used into, maxo or intb
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	95 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	96 dataMatrix <- featureValues(xdata, method="medret", value=intval)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	97 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	98 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	99 variableMetadata <- featureDefinitions(xdata)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	100 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	101 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	102
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	103 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	104 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	105
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	106 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	107 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	108
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	109 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	110
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	111 #@author G. Le Corguille
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	112 getPlotChromatogram <- function(xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	113
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	114 chrom <- chromatogram(xdata, aggregationFun = aggregationFun)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	115 if (aggregationFun == "sum")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	116 type="Total Ion Chromatograms"
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	117 else
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	118 type="Base Peak Intensity Chromatograms"
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	119
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	120 adjusted="Raw"
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	121 if (hasAdjustedRtime(xdata))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	122 adjusted="Adjusted"
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	123
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	124 main <- paste(type,":",adjusted,"data")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	125
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	126 pdf(pdfname, width=16, height=10)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	127
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	128 # Color by group
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	129 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	130 names(group_colors) <- unique(xdata$sample_group)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	131 plot(chrom, col = group_colors[chrom$sample_group], main=main)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	132 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	133
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	134 # Color by sample
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	135 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	136 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	137
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	138 dev.off()
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	139 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	140
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	141 #@author G. Le Corguille
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	142 getPlotTICs <- function(xdata, pdfname="TICs.pdf") {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	143 getPlotChromatogram(xdata, pdfname, aggregationFun = "sum")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	144 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	145
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	146 #@author G. Le Corguille
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	147 getPlotBPIs <- function(xdata, pdfname="BPIs.pdf") {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	148 getPlotChromatogram(xdata, pdfname, aggregationFun = "max")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	149 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	150
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	151
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	152 # Get the polarities from all the samples of a condition
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	153 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	154 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	155 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	156 cat("Creating the sampleMetadata file...\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	157
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	158 #Create the sampleMetada dataframe
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	159 sampleMetadata <- xdata@phenoData@data
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	160 rownames(sampleMetadata) <- NULL
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	161 colnames(sampleMetadata) <- c("sampleMetadata", "class")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	162
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	163 sampleNamesOrigin <- sampleMetadata$sampleMetadata
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	164 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	165
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	166 if (any(duplicated(sampleNamesMakeNames))) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	167 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())
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	168 for (sampleName in sampleNamesOrigin) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	169 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	170 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	171 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	172 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	173
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	174 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	175 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")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	176 for (sampleName in sampleNamesOrigin) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	177 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	178 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	179 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	180
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	181 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	182
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	183
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	184 #For each sample file, the following actions are done
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	185 for (fileIdx in 1:length(fileNames(xdata))) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	186 #Check if the file is in the CDF format
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	187 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	188
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	189 # If the column isn't exist, with add one filled with NA
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	190 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	191
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	192 #Extract the polarity (a list of polarities)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	193 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	194 #Verify if all the scans have the same polarity
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	195 uniq_list <- unique(polarity)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	196 if (length(uniq_list)>1){
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	197 polarity <- "mixed"
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	198 } else {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	199 polarity <- as.character(uniq_list)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	200 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	201
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	202 #Set the polarity attribute
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	203 sampleMetadata$polarity[fileIdx] <- polarity
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	204 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	205
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	206 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	207
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	208 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	209
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	210 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	211
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	212 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	213
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	214
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	215 # This function check if xcms will found all the files
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	216 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	217 checkFilesCompatibilityWithXcms <- function(directory) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	218 cat("Checking files filenames compatibilities with xmcs...\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	219 # WHAT XCMS WILL FIND
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	220 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	221 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	222 info <- file.info(directory)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	223 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	224 files <- c(directory[!info$isdir], listed)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	225 files_abs <- file.path(getwd(), files)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	226 exists <- file.exists(files_abs)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	227 files[exists] <- files_abs[exists]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	228 files[exists] <- sub("//","/",files[exists])
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	229
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	230 # WHAT IS ON THE FILESYSTEM
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	231 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.' -not -path 'conda-env' -type f -name \"\""), intern=T)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	232 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	233
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	234 # COMPARISON
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	235 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	236 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	237 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	238 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	239 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	240 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	241
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	242
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	243 #This function list the compatible files within the directory as xcms did
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	244 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	245 getMSFiles <- function (directory) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	246 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	247 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	248 info <- file.info(directory)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	249 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	250 files <- c(directory[!info$isdir], listed)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	251 exists <- file.exists(files)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	252 files <- files[exists]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	253 return(files)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	254 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	255
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	256 # This function check if XML contains special caracters. It also checks integrity and completness.
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	257 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	258 checkXmlStructure <- function (directory) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	259 cat("Checking XML structure...\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	260
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	261 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;")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	262 capture <- system(cmd, intern=TRUE)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	263
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	264 if (length(capture)>0){
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	265 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	266 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	267 write(capture, stderr())
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	268 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	269 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	270
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	271 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	272
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	273
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	274 # This function check if XML contain special characters
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	275 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	276 deleteXmlBadCharacters<- function (directory) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	277 cat("Checking Non ASCII characters in the XML...\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	278
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	279 processed <- F
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	280 l <- system( paste0("find '",directory, "' -not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'"), intern=TRUE)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	281 for (i in l){
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	282 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	283 capture <- suppressWarnings(system(cmd, intern=TRUE))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	284 if (length(capture)>0){
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	285 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	286 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	287 c <- system(cmd, intern=TRUE)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	288 capture <- ""
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	289 processed <- T
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	290 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	291 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	292 if (processed) cat("\n\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	293 return(processed)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	294 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	295
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	296
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	297 # This function will compute MD5 checksum to check the data integrity
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	298 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	299 getMd5sum <- function (directory) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	300 cat("Compute md5 checksum...\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	301 # WHAT XCMS WILL FIND
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	302 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	303 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	304 info <- file.info(directory)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	305 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	306 files <- c(directory[!info$isdir], listed)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	307 exists <- file.exists(files)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	308 files <- files[exists]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	309
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	310 library(tools)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	311
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	312 #cat("\n\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	313
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	314 return(as.matrix(md5sum(files)))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	315 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	316
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	317
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	318 # This function get the raw file path from the arguments
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	319 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	320 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	321 if (!is.null(args$zipfile)) zipfile <- args$zipfile
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	322 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	323 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	324
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	325 if (!is.null(args$singlefile_galaxyPath)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	326 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	327 singlefile_sampleNames <- args$singlefile_sampleName
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	328 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	329 if (!is.null(args$singlefile_galaxyPathPositive)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	330 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	331 singlefile_sampleNames <- args$singlefile_sampleNamePositive
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	332 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	333 if (!is.null(args$singlefile_galaxyPathNegative)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	334 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	335 singlefile_sampleNames <- args$singlefile_sampleNameNegative
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	336 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	337 if (exists("singlefile_galaxyPaths")){
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	338 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\\|"))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	339 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\\|"))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	340
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	341 singlefile <- NULL
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	342 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	343 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	344 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	345 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	346 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	347 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	348 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	349 args[[argument]] <- NULL
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	350 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	351 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	352 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	353
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	354
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	355 # This function retrieve the raw file in the working directory
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	356 # - if zipfile: unzip the file with its directory tree
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	357 # - if singlefiles: set symlink with the good filename
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	358 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	359 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	360 if(!is.null(singlefile) && (length("singlefile")>0)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	361 for (singlefile_sampleName in names(singlefile)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	362 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	363 if(!file.exists(singlefile_galaxyPath)){
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	364 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	365 print(error_message); stop(error_message)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	366 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	367
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	368 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	369 file.copy(singlefile_galaxyPath, singlefile_sampleName)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	370
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	371 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	372 directory <- "."
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	373
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	374 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	375 if(!is.null(zipfile) && (zipfile != "")) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	376 if(!file.exists(zipfile)){
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	377 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	378 print(error_message)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	379 stop(error_message)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	380 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	381
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	382 #list all file in the zip file
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	383 #zip_files <- unzip(zipfile,list=T)[,"Name"]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	384
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	385 #unzip
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	386 suppressWarnings(unzip(zipfile, unzip="unzip"))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	387
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	388 #get the directory name
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	389 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	390 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	391 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	392 directory <- "."
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	393 if (length(directories) == 1) directory <- directories
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	394
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	395 cat("files_root_directory\t",directory,"\n")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	396
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	397 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	398 return (directory)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	399 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	400
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	401
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	402 # This function retrieve a xset like object
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	403 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	404 getxcmsSetObject <- function(xobject) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	405 # XCMS 1.x
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	406 if (class(xobject) == "xcmsSet")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	407 return (xobject)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	408 # XCMS 3.x
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	409 if (class(xobject) == "XCMSnExp") {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	410 # Get the legacy xcmsSet object
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	411 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	412 sampclass(xset) <- xset@phenoData$sample_group
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	413 return (xset)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	414 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	415 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	416
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	417
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	418 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	419 # https://github.com/sneumann/xcms/issues/250
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	420 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	421 mzfmt <- paste("%.", mzdec, "f", sep = "")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	422 rtfmt <- paste("%.", rtdec, "f", sep = "")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	423
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	424 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	425 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	426
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	427 if (any(dup <- duplicated(gnames)))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	428 for (dupname in unique(gnames[dup])) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	429 dupidx <- which(gnames == dupname)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	430 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	431 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	432
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	433 return (gnames)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	434 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	435
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	436 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	437 # https://github.com/sneumann/xcms/issues/247
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	438 .concatenate_XCMSnExp <- function(...) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	439 x <- list(...)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	440 if (length(x) == 0)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	441 return(NULL)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	442 if (length(x) == 1)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	443 return(x[[1]])
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	444 ## Check that all are XCMSnExp objects.
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	445 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	446 stop("All passed objects should be 'XCMSnExp' objects")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	447 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	448 ## If any of the XCMSnExp has alignment results or detected features drop
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	449 ## them!
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	450 x <- lapply(x, function(z) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	451 if (hasAdjustedRtime(z)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	452 z <- dropAdjustedRtime(z)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	453 warning("Adjusted retention times found, had to drop them.")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	454 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	455 if (hasFeatures(z)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	456 z <- dropFeatureDefinitions(z)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	457 warning("Feature definitions found, had to drop them.")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	458 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	459 z
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	460 })
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	461 ## Combine peaks
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	462 fls <- lapply(x, fileNames)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	463 startidx <- cumsum(lengths(fls))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	464 pks <- lapply(x, chromPeaks)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	465 procH <- lapply(x, processHistory)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	466 for (i in 2:length(fls)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	467 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	468 procH[[i]] <- lapply(procH[[i]], function(z) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	469 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	470 z
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	471 })
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	472 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	473 pks <- do.call(rbind, pks)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	474 new_x@.processHistory <- unlist(procH)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	475 chromPeaks(new_x) <- pks
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	476 if (validObject(new_x))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	477 new_x
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	478 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	479
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	480 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	481 # https://github.com/sneumann/xcms/issues/247
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	482 .concatenate_OnDiskMSnExp <- function(...) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	483 x <- list(...)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	484 if (length(x) == 0)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	485 return(NULL)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	486 if (length(x) == 1)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	487 return(x[[1]])
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	488 ## Check that all are XCMSnExp objects.
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	489 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	490 stop("All passed objects should be 'OnDiskMSnExp' objects")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	491 ## Check processingQueue
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	492 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	493 new_procQ <- procQ[[1]]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	494 is_ok <- unlist(lapply(procQ, function(z)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	495 !is.character(all.equal(new_procQ, z))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	496 ))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	497 if (any(!is_ok)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	498 warning("Processing queues from the submitted objects differ! ",
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	499 "Dropping the processing queue.")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	500 new_procQ <- list()
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	501 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	502 ## processingData
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	503 fls <- lapply(x, function(z) z@processingData@files)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	504 startidx <- cumsum(lengths(fls))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	505 ## featureData
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	506 featd <- lapply(x, fData)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	507 ## Have to update the file index and the spectrum names.
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	508 for (i in 2:length(featd)) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	509 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	510 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	511 fileIds = featd[[i]]$fileIdx,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	512 spectrumIds = featd[[i]]$spIdx,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	513 nSpectra = nrow(featd[[i]]),
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	514 nFiles = length(unlist(fls))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	515 )
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	516 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	517 featd <- do.call(rbind, featd)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	518 featd$spectrum <- 1:nrow(featd)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	519 ## experimentData
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	520 expdata <- lapply(x, function(z) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	521 ed <- z@experimentData
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	522 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	523 instrumentModel = ed@instrumentModel,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	524 ionSource = ed@ionSource,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	525 analyser = ed@analyser,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	526 detectorType = ed@detectorType,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	527 stringsAsFactors = FALSE)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	528 })
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	529 expdata <- do.call(rbind, expdata)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	530 expdata <- new("MIAPE",
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	531 instrumentManufacturer = expdata$instrumentManufacturer,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	532 instrumentModel = expdata$instrumentModel,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	533 ionSource = expdata$ionSource,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	534 analyser = expdata$analyser,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	535 detectorType = expdata$detectorType)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	536
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	537 ## protocolData
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	538 protodata <- lapply(x, function(z) z@protocolData)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	539 if (any(unlist(lapply(protodata, nrow)) > 0))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	540 warning("Found non-empty protocol data, but merging protocol data is",
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	541 " currently not supported. Skipped.")
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	542 ## phenoData
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	543 pdata <- do.call(rbind, lapply(x, pData))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	544 res <- new(
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	545 "OnDiskMSnExp",
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	546 phenoData = new("NAnnotatedDataFrame", data = pdata),
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	547 featureData = new("AnnotatedDataFrame", featd),
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	548 processingData = new("MSnProcess",
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	549 processing = paste0("Concatenated [", date(), "]"),
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	550 files = unlist(fls), smoothed = NA),
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	551 experimentData = expdata,
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	552 spectraProcessingQueue = new_procQ)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	553 if (validObject(res))
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	554 res
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	555 }
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	556
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	557 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	558 # https://github.com/sneumann/xcms/issues/247
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	559 c.XCMSnExp <- function(...) {
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	560 .concatenate_XCMSnExp(...)
fe1f0f16d9e6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cfb08142b6bfb78002b4e0d7775adb1a58e66c33-dirty lecorguille parents: diff changeset	561 }

Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate lib.r @ 1:86ff4497b871 draft