Mercurial > repos > lecorguille > xcms_retcor
diff lib.r @ 30:4d6f4cd7c3ef draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
| author | lecorguille |
|---|---|
| date | Thu, 01 Mar 2018 04:16:45 -0500 |
| parents | c013ed353a2f |
| children | 281786a7b9a2 |
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--- a/lib.r Tue Feb 13 04:44:03 2018 -0500 +++ b/lib.r Thu Mar 01 04:16:45 2018 -0500 @@ -1,54 +1,105 @@ -#Authors ABiMS TEAM -#Lib.r for Galaxy Workflow4Metabolomics xcms tools -# -#version 2.4: lecorguille -# add getPeaklistW4M -#version 2.3: yguitton -# correction for empty PDF when only 1 class -#version 2.2 -# correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet -# Note if scanrange is used a warning is prompted in R console but do not stop PDF generation -#version 2.1: yguitton -# Modifications made by Guitton Yann +#@authors ABiMS TEAM, Y. Guitton +# lib.r for Galaxy Workflow4Metabolomics xcms tools +#@author G. Le Corguille +# solve an issue with batch if arguments are logical TRUE/FALSE +parseCommandArgs <- function(...) { + args <- batch::parseCommandArgs(...) + for (key in names(args)) { + if (args[key] %in% c("TRUE","FALSE")) + args[key] = as.logical(args[key]) + } + return(args) +} #@author G. Le Corguille -#This function convert if it is required the Retention Time in minutes +# This function will +# - load the packages +# - display the sessionInfo +loadAndDisplayPackages <- function(pkgs) { + for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) + + sessioninfo = sessionInfo() + cat(sessioninfo$R.version$version.string,"\n") + cat("Main packages:\n") + for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") + cat("Other loaded packages:\n") + for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") +} + +#@author G. Le Corguille +# This function convert if it is required the Retention Time in minutes RTSecondToMinute <- function(variableMetadata, convertRTMinute) { if (convertRTMinute){ #converting the retention times (seconds) into minutes print("converting the retention times into minutes in the variableMetadata") - variableMetadata[,"rt"]=variableMetadata[,"rt"]/60 - variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60 - variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60 + variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60 + variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60 + variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60 } return (variableMetadata) } #@author G. Le Corguille -#This function format ions identifiers +# This function format ions identifiers formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) { - splitDeco = strsplit(as.character(variableMetadata$name),"_") - idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) - namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) - variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) + splitDeco <- strsplit(as.character(variableMetadata$name),"_") + idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) + namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) + variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) return(variableMetadata) } #@author G. Le Corguille +# Draw the plotChromPeakDensity 3 per page in a pdf file +getPlotChromPeakDensity <- function(xdata) { + pdf(file="plotChromPeakDensity.pdf", width=16, height=12) + + par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5)) + + group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] + names(group_colors) <- unique(xdata$sample_group) + + xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) + for (i in 1:nrow(featureDefinitions(xdata))) { + plotChromPeakDensity(xdata, mz=c(featureDefinitions(xdata)[i,]$mzmin,featureDefinitions(xdata)[i,]$mzmax), col=group_colors, pch=16, xlim=xlim) + legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) + } + + dev.off() +} + +#@author G. Le Corguille +# Draw the plotChromPeakDensity 3 per page in a pdf file +getPlotAdjustedRtime <- function(xdata) { + pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12) + # Color by group + group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] + names(group_colors) <- unique(xdata$sample_group) + plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group]) + legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) + # Color by sample + plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name))) + legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1) + dev.off() +} + +#@author G. Le Corguille # value: intensity values to be used into, maxo or intb -getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) { - variableMetadata_dataMatrix = peakTable(xset, method="medret", value=intval) - variableMetadata_dataMatrix = cbind(name=groupnames(xset),variableMetadata_dataMatrix) +getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) { + dataMatrix <- featureValues(xdata, method="medret", value=intval) + colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix)) + dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix) + variableMetadata <- featureDefinitions(xdata) + colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" + variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata) - dataMatrix = variableMetadata_dataMatrix[,(make.names(colnames(variableMetadata_dataMatrix)) %in% c("name", make.names(sampnames(xset))))] - - variableMetadata = variableMetadata_dataMatrix[,!(make.names(colnames(variableMetadata_dataMatrix)) %in% c(make.names(sampnames(xset))))] - variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute) - variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) + variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) + variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) + } #@author Y. Guitton @@ -70,11 +121,11 @@ files <- filepaths(xcmsSet) } - phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class + phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class - classnames<-vector("list",length(phenoDataClass)) + classnames <- vector("list",length(phenoDataClass)) for (i in 1:length(phenoDataClass)){ - classnames[[i]]<-which( xcmsSet@phenoData[,1]==phenoDataClass[i]) + classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i]) } N <- dim(phenoData(xcmsSet))[1] @@ -101,12 +152,12 @@ pdf(pdfname,w=16,h=10) cols <- rainbow(N) - lty = 1:N - pch = 1:N + lty <- 1:N + pch <- 1:N #search for max x and max y in BPCs - xlim = range(sapply(TIC, function(x) range(x[,1]))) - ylim = range(sapply(TIC, function(x) range(x[,2]))) - ylim = c(-ylim[2], ylim[2]) + xlim <- range(sapply(TIC, function(x) range(x[,1]))) + ylim <- range(sapply(TIC, function(x) range(x[,2]))) + ylim <- c(-ylim[2], ylim[2]) ##plot start @@ -115,63 +166,63 @@ for (k in 1:(length(phenoDataClass)-1)){ for (l in (k+1):length(phenoDataClass)){ #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" ")) - plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC") - colvect<-NULL + plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC") + colvect <- NULL for (j in 1:length(classnames[[k]])) { tic <- TIC[[classnames[[k]][j]]] - # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") - points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") - colvect<-append(colvect,cols[classnames[[k]][j]]) + # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") + points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") + colvect <- append(colvect,cols[classnames[[k]][j]]) } for (j in 1:length(classnames[[l]])) { - # i=class2names[j] + # i <- class2names[j] tic <- TIC[[classnames[[l]][j]]] - points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") - colvect<-append(colvect,cols[classnames[[l]][j]]) + points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l") + colvect <- append(colvect,cols[classnames[[l]][j]]) } - legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) + legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch) } } }#end if length >2 if (length(phenoDataClass)==2){ - k=1 - l=2 - colvect<-NULL - plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC") + k <- 1 + l <- 2 + colvect <- NULL + plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="BPC") for (j in 1:length(classnames[[k]])) { tic <- TIC[[classnames[[k]][j]]] - # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") - points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") + # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") + points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") colvect<-append(colvect,cols[classnames[[k]][j]]) } for (j in 1:length(classnames[[l]])) { - # i=class2names[j] + # i <- class2names[j] tic <- TIC[[classnames[[l]][j]]] - points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") - colvect<-append(colvect,cols[classnames[[l]][j]]) + points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l") + colvect <- append(colvect,cols[classnames[[l]][j]]) } - legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) + legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch) }#end length ==2 #case where only one class if (length(phenoDataClass)==1){ - k=1 - ylim = range(sapply(TIC, function(x) range(x[,2]))) - colvect<-NULL - plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k], sep=""), xlab = "Retention Time (min)", ylab = "BPC") + k <- 1 + ylim <- range(sapply(TIC, function(x) range(x[,2]))) + colvect <- NULL + plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Base Peak Chromatograms \n","BPCs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="BPC") for (j in 1:length(classnames[[k]])) { tic <- TIC[[classnames[[k]][j]]] - # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") - points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") - colvect<-append(colvect,cols[classnames[[k]][j]]) + # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") + points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") + colvect <- append(colvect,cols[classnames[[k]][j]]) } - legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch) + legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch) }#end length ==1 @@ -183,34 +234,32 @@ #@author Y. Guitton -getTIC <- function(file,rtcor=NULL) { +getTIC <- function(file, rtcor=NULL) { object <- xcmsRaw(file) - cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity) + cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object, mzrange=range(object@env$mz))$intensity) } -## -## overlay TIC from all files in current folder or from xcmsSet, create pdf -## +#overlay TIC from all files in current folder or from xcmsSet, create pdf #@author Y. Guitton -getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) { +getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf", rt=c("raw","corrected")) { cat("Creating TIC pdf...\n") if (is.null(xcmsSet)) { filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") - filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|") + filepattern <- paste(paste("\\.", filepattern, "$", sep=""), collapse="|") if (is.null(files)) files <- getwd() info <- file.info(files) - listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE) + listed <- list.files(files[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) files <- c(files[!info$isdir], listed) } else { files <- filepaths(xcmsSet) } - phenoDataClass<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class - classnames<-vector("list",length(phenoDataClass)) + phenoDataClass <- as.vector(levels(xcmsSet@phenoData[,"class"])) #sometime phenoData have more than 1 column use first as class + classnames <- vector("list",length(phenoDataClass)) for (i in 1:length(phenoDataClass)){ - classnames[[i]]<-which( xcmsSet@phenoData[,1]==phenoDataClass[i]) + classnames[[i]] <- which( xcmsSet@phenoData[,"class"]==phenoDataClass[i]) } N <- length(files) @@ -220,17 +269,17 @@ if (!is.null(xcmsSet) && rt == "corrected") rtcor <- xcmsSet@rt$corrected[[i]] else rtcor <- NULL - TIC[[i]] <- getTIC(files[i],rtcor=rtcor) + TIC[[i]] <- getTIC(files[i], rtcor=rtcor) } - pdf(pdfname,w=16,h=10) + pdf(pdfname, w=16, h=10) cols <- rainbow(N) - lty = 1:N - pch = 1:N + lty <- 1:N + pch <- 1:N #search for max x and max y in TICs - xlim = range(sapply(TIC, function(x) range(x[,1]))) - ylim = range(sapply(TIC, function(x) range(x[,2]))) - ylim = c(-ylim[2], ylim[2]) + xlim <- range(sapply(TIC, function(x) range(x[,1]))) + ylim <- range(sapply(TIC, function(x) range(x[,2]))) + ylim <- c(-ylim[2], ylim[2]) ##plot start @@ -238,61 +287,61 @@ for (k in 1:(length(phenoDataClass)-1)){ for (l in (k+1):length(phenoDataClass)){ #print(paste(phenoDataClass[k],"vs",phenoDataClass[l],sep=" ")) - plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC") - colvect<-NULL + plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k]," vs ",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC") + colvect <- NULL for (j in 1:length(classnames[[k]])) { tic <- TIC[[classnames[[k]][j]]] - # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") - points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") - colvect<-append(colvect,cols[classnames[[k]][j]]) + # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") + points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") + colvect <- append(colvect,cols[classnames[[k]][j]]) } for (j in 1:length(classnames[[l]])) { # i=class2names[j] tic <- TIC[[classnames[[l]][j]]] - points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") - colvect<-append(colvect,cols[classnames[[l]][j]]) + points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l") + colvect <- append(colvect,cols[classnames[[l]][j]]) } - legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) + legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch) } } }#end if length >2 if (length(phenoDataClass)==2){ - k=1 - l=2 + k <- 1 + l <- 2 - plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC") - colvect<-NULL + plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k],"vs",phenoDataClass[l], sep=""), xlab="Retention Time (min)", ylab="TIC") + colvect <- NULL for (j in 1:length(classnames[[k]])) { tic <- TIC[[classnames[[k]][j]]] - # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") - points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") - colvect<-append(colvect,cols[classnames[[k]][j]]) + # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") + points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") + colvect <- append(colvect,cols[classnames[[k]][j]]) } for (j in 1:length(classnames[[l]])) { - # i=class2names[j] + # i <- class2names[j] tic <- TIC[[classnames[[l]][j]]] - points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") - colvect<-append(colvect,cols[classnames[[l]][j]]) + points(tic[,1]/60, -tic[,2], col=cols[classnames[[l]][j]], pch=pch[classnames[[l]][j]], type="l") + colvect <- append(colvect,cols[classnames[[l]][j]]) } - legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) + legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col=colvect, lty=lty, pch=pch) }#end length ==2 #case where only one class if (length(phenoDataClass)==1){ - k=1 - ylim = range(sapply(TIC, function(x) range(x[,2]))) + k <- 1 + ylim <- range(sapply(TIC, function(x) range(x[,2]))) - plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k], sep=""), xlab = "Retention Time (min)", ylab = "TIC") - colvect<-NULL + plot(0, 0, type="n", xlim=xlim/60, ylim=ylim, main=paste("Total Ion Chromatograms \n","TICs_",phenoDataClass[k], sep=""), xlab="Retention Time (min)", ylab="TIC") + colvect <- NULL for (j in 1:length(classnames[[k]])) { tic <- TIC[[classnames[[k]][j]]] - # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") - points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") - colvect<-append(colvect,cols[classnames[[k]][j]]) + # points(tic[,1]/60, tic[,2], col=cols[i], pch=pch[i], type="l") + points(tic[,1]/60, tic[,2], col=cols[classnames[[k]][j]], pch=pch[classnames[[k]][j]], type="l") + colvect <- append(colvect,cols[classnames[[k]][j]]) } - legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch) + legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch) }#end length ==1 @@ -303,17 +352,19 @@ -## -## Get the polarities from all the samples of a condition +# Get the polarities from all the samples of a condition #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM -getSampleMetadata <- function(xcmsSet=NULL, sampleMetadataOutput="sampleMetadata.tsv") { +getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") { cat("Creating the sampleMetadata file...\n") #Create the sampleMetada dataframe - sampleMetadata=xset@phenoData - sampleNamesOrigin=rownames(sampleMetadata) - sampleNamesMakeNames=make.names(sampleNamesOrigin) + sampleMetadata <- xdata@phenoData@data + rownames(sampleMetadata) <- NULL + colnames(sampleMetadata) <- c("sampleMetadata", "class") + + sampleNamesOrigin <- sampleMetadata$sampleMetadata + sampleNamesMakeNames <- make.names(sampleNamesOrigin) if (any(duplicated(sampleNamesMakeNames))) { write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr()) @@ -330,63 +381,49 @@ } } - sampleMetadata$sampleMetadata=sampleNamesMakeNames - sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns - rownames(sampleMetadata)=NULL + sampleMetadata$sampleMetadata <- sampleNamesMakeNames + - #Create a list of files name in the current directory - list_files=xset@filepaths #For each sample file, the following actions are done - for (file in list_files){ + for (fileIdx in 1:length(fileNames(xdata))) { #Check if the file is in the CDF format - if (!mzR:::netCDFIsFile(file)){ + if (!mzR:::netCDFIsFile(fileNames(xdata))) { # If the column isn't exist, with add one filled with NA - if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA + if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA - #Create a simple xcmsRaw object for each sample - xcmsRaw=xcmsRaw(file) #Extract the polarity (a list of polarities) - polarity=xcmsRaw@polarity + polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"] #Verify if all the scans have the same polarity - uniq_list=unique(polarity) + uniq_list <- unique(polarity) if (length(uniq_list)>1){ - polarity="mixed" + polarity <- "mixed" } else { - polarity=as.character(uniq_list) + polarity <- as.character(uniq_list) } - #Transforms the character to obtain only the sample name - filename=basename(file) - library(tools) - samplename=file_path_sans_ext(filename) #Set the polarity attribute - sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity - - #Delete xcmsRaw object because it creates a bug for the fillpeaks step - rm(xcmsRaw) + sampleMetadata$polarity[fileIdx] <- polarity } } write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) - return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames)) + return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames)) } -## -## This function check if xcms will found all the files -## +# This function check if xcms will found all the files #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM checkFilesCompatibilityWithXcms <- function(directory) { cat("Checking files filenames compatibilities with xmcs...\n") # WHAT XCMS WILL FIND filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") - filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|") + filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") info <- file.info(directory) - listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE) + listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) files <- c(directory[!info$isdir], listed) files_abs <- file.path(getwd(), files) exists <- file.exists(files_abs) @@ -394,8 +431,8 @@ files[exists] <- sub("//","/",files[exists]) # WHAT IS ON THE FILESYSTEM - filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T) - filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] + filesystem_filepaths <- system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T) + filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] # COMPARISON if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { @@ -406,16 +443,26 @@ } +#This function list the compatible files within the directory as xcms did +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM +getMSFiles <- function (directory) { + filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") + filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") + info <- file.info(directory) + listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE) + files <- c(directory[!info$isdir], listed) + exists <- file.exists(files) + files <- files[exists] + return(files) +} -## -## This function check if XML contains special caracters. It also checks integrity and completness. -## +# This function check if XML contains special caracters. It also checks integrity and completness. #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM checkXmlStructure <- function (directory) { cat("Checking XML structure...\n") - cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;") - capture=system(cmd,intern=TRUE) + cmd <- paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;") + capture <- system(cmd, intern=TRUE) if (length(capture)>0){ #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) @@ -427,24 +474,22 @@ } -## -## This function check if XML contain special characters -## +# This function check if XML contain special characters #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM deleteXmlBadCharacters<- function (directory) { cat("Checking Non ASCII characters in the XML...\n") - processed=F - l=system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"),intern=TRUE) + processed <- F + l <- system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE) for (i in l){ - cmd=paste("LC_ALL=C grep '[^ -~]' \"",i,"\"",sep="") - capture=suppressWarnings(system(cmd,intern=TRUE)) + cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="") + capture <- suppressWarnings(system(cmd, intern=TRUE)) if (length(capture)>0){ - cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) + cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") ) - c=system(cmd,intern=TRUE) - capture="" - processed=T + c <- system(cmd, intern=TRUE) + capture <- "" + processed <- T } } if (processed) cat("\n\n") @@ -452,17 +497,15 @@ } -## -## This function will compute MD5 checksum to check the data integrity -## +# This function will compute MD5 checksum to check the data integrity #@author Gildas Le Corguille lecorguille@sb-roscoff.fr getMd5sum <- function (directory) { cat("Compute md5 checksum...\n") # WHAT XCMS WILL FIND filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") - filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|") + filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") info <- file.info(directory) - listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE) + listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) files <- c(directory[!info$isdir], listed) exists <- file.exists(files) files <- files[exists] @@ -476,80 +519,246 @@ # This function get the raw file path from the arguments -getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) { - if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]] - if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]] - if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]] +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +getRawfilePathFromArguments <- function(singlefile, zipfile, args) { + if (!is.null(args$zipfile)) zipfile <- args$zipfile + if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive + if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative - if (!is.null(listArguments[["singlefile_galaxyPath"]])) { - singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]]; - singlefile_sampleNames = listArguments[["singlefile_sampleName"]] + if (!is.null(args$singlefile_galaxyPath)) { + singlefile_galaxyPaths <- args$singlefile_galaxyPath; + singlefile_sampleNames <- args$singlefile_sampleName } - if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) { - singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]]; - singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]] + if (!is.null(args$singlefile_galaxyPathPositive)) { + singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive; + singlefile_sampleNames <- args$singlefile_sampleNamePositive } - if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) { - singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]]; - singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]] + if (!is.null(args$singlefile_galaxyPathNegative)) { + singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative; + singlefile_sampleNames <- args$singlefile_sampleNameNegative } if (exists("singlefile_galaxyPaths")){ - singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,",")) - singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,",")) + singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,",")) + singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,",")) - singlefile=NULL + singlefile <- NULL for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { - singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i] - singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i] - singlefile[[singlefile_sampleName]] = singlefile_galaxyPath + singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] + singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] + singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath } } for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) { - listArguments[[argument]]=NULL + args[[argument]] <- NULL } - return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments)) + return(list(zipfile=zipfile, singlefile=singlefile, args=args)) } # This function retrieve the raw file in the working directory # - if zipfile: unzip the file with its directory tree # - if singlefiles: set symlink with the good filename +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) { if(!is.null(singlefile) && (length("singlefile")>0)) { for (singlefile_sampleName in names(singlefile)) { - singlefile_galaxyPath = singlefile[[singlefile_sampleName]] + singlefile_galaxyPath <- singlefile[[singlefile_sampleName]] if(!file.exists(singlefile_galaxyPath)){ - error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") + error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") print(error_message); stop(error_message) } - file.symlink(singlefile_galaxyPath,singlefile_sampleName) + if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T))) + file.copy(singlefile_galaxyPath, singlefile_sampleName) + } - directory = "." + directory <- "." } - if(!is.null(zipfile) && (zipfile!="")) { + if(!is.null(zipfile) && (zipfile != "")) { if(!file.exists(zipfile)){ - error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") + error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") print(error_message) stop(error_message) } #list all file in the zip file - #zip_files=unzip(zipfile,list=T)[,"Name"] + #zip_files <- unzip(zipfile,list=T)[,"Name"] #unzip suppressWarnings(unzip(zipfile, unzip="unzip")) #get the directory name - filesInZip=unzip(zipfile, list=T); - directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); - directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] - directory = "." - if (length(directories) == 1) directory = directories + suppressWarnings(filesInZip <- unzip(zipfile, list=T)) + directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))) + directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] + directory <- "." + if (length(directories) == 1) directory <- directories cat("files_root_directory\t",directory,"\n") } return (directory) } + + +# This function retrieve a xset like object +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +getxcmsSetObject <- function(xobject) { + # XCMS 1.x + if (class(xobject) == "xcmsSet") + return (xobject) + # XCMS 3.x + if (class(xobject) == "XCMSnExp") { + # Get the legacy xcmsSet object + suppressWarnings(xset <- as(xobject, 'xcmsSet')) + sampclass(xset) <- xset@phenoData$sample_group + return (xset) + } +} + + +#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 +# https://github.com/sneumann/xcms/issues/250 +groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) { + mzfmt <- paste("%.", mzdec, "f", sep = "") + rtfmt <- paste("%.", rtdec, "f", sep = "") + + gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T", + sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "") + + if (any(dup <- duplicated(gnames))) + for (dupname in unique(gnames[dup])) { + dupidx <- which(gnames == dupname) + gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_") + } + + return (gnames) +} + +#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 +# https://github.com/sneumann/xcms/issues/247 +.concatenate_XCMSnExp <- function(...) { + x <- list(...) + if (length(x) == 0) + return(NULL) + if (length(x) == 1) + return(x[[1]]) + ## Check that all are XCMSnExp objects. + if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp"))))) + stop("All passed objects should be 'XCMSnExp' objects") + new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp") + ## If any of the XCMSnExp has alignment results or detected features drop + ## them! + x <- lapply(x, function(z) { + if (hasAdjustedRtime(z)) { + z <- dropAdjustedRtime(z) + warning("Adjusted retention times found, had to drop them.") + } + if (hasFeatures(z)) { + z <- dropFeatureDefinitions(z) + warning("Feature definitions found, had to drop them.") + } + z + }) + ## Combine peaks + fls <- lapply(x, fileNames) + startidx <- cumsum(lengths(fls)) + pks <- lapply(x, chromPeaks) + procH <- lapply(x, processHistory) + for (i in 2:length(fls)) { + pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1] + procH[[i]] <- lapply(procH[[i]], function(z) { + z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1]) + z + }) + } + pks <- do.call(rbind, pks) + new_x@.processHistory <- unlist(procH) + chromPeaks(new_x) <- pks + if (validObject(new_x)) + new_x +} + +#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 +# https://github.com/sneumann/xcms/issues/247 +.concatenate_OnDiskMSnExp <- function(...) { + x <- list(...) + if (length(x) == 0) + return(NULL) + if (length(x) == 1) + return(x[[1]]) + ## Check that all are XCMSnExp objects. + if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp"))))) + stop("All passed objects should be 'OnDiskMSnExp' objects") + ## Check processingQueue + procQ <- lapply(x, function(z) z@spectraProcessingQueue) + new_procQ <- procQ[[1]] + is_ok <- unlist(lapply(procQ, function(z) + !is.character(all.equal(new_procQ, z)) + )) + if (any(!is_ok)) { + warning("Processing queues from the submitted objects differ! ", + "Dropping the processing queue.") + new_procQ <- list() + } + ## processingData + fls <- lapply(x, function(z) z@processingData@files) + startidx <- cumsum(lengths(fls)) + ## featureData + featd <- lapply(x, fData) + ## Have to update the file index and the spectrum names. + for (i in 2:length(featd)) { + featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1] + rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames( + fileIds = featd[[i]]$fileIdx, + spectrumIds = featd[[i]]$spIdx, + nSpectra = nrow(featd[[i]]), + nFiles = length(unlist(fls)) + ) + } + featd <- do.call(rbind, featd) + featd$spectrum <- 1:nrow(featd) + ## experimentData + expdata <- lapply(x, function(z) { + ed <- z@experimentData + data.frame(instrumentManufacturer = ed@instrumentManufacturer, + instrumentModel = ed@instrumentModel, + ionSource = ed@ionSource, + analyser = ed@analyser, + detectorType = ed@detectorType, + stringsAsFactors = FALSE) + }) + expdata <- do.call(rbind, expdata) + expdata <- new("MIAPE", + instrumentManufacturer = expdata$instrumentManufacturer, + instrumentModel = expdata$instrumentModel, + ionSource = expdata$ionSource, + analyser = expdata$analyser, + detectorType = expdata$detectorType) + + ## protocolData + protodata <- lapply(x, function(z) z@protocolData) + if (any(unlist(lapply(protodata, nrow)) > 0)) + warning("Found non-empty protocol data, but merging protocol data is", + " currently not supported. Skipped.") + ## phenoData + pdata <- do.call(rbind, lapply(x, pData)) + res <- new( + "OnDiskMSnExp", + phenoData = new("NAnnotatedDataFrame", data = pdata), + featureData = new("AnnotatedDataFrame", featd), + processingData = new("MSnProcess", + processing = paste0("Concatenated [", date(), "]"), + files = unlist(fls), smoothed = NA), + experimentData = expdata, + spectraProcessingQueue = new_procQ) + if (validObject(res)) + res +} + +#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 +# https://github.com/sneumann/xcms/issues/247 +c.XCMSnExp <- function(...) { + .concatenate_XCMSnExp(...) +}