Mercurial > repos > lecorguille > xcms_summary
diff lib.r @ 29:3d4339594010 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
| author | lecorguille |
|---|---|
| date | Thu, 01 Mar 2018 04:17:50 -0500 |
| parents | |
| children | 17562a6799a1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib.r Thu Mar 01 04:17:50 2018 -0500 @@ -0,0 +1,764 @@ +#@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 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 + } + return (variableMetadata) +} + +#@author G. Le Corguille +# 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"))]) + 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(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) + + 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 +getBPC <- function(file,rtcor=NULL, ...) { + object <- xcmsRaw(file) + sel <- profRange(object, ...) + cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE])) + #plotChrom(xcmsRaw(file), base=T) +} + +#@author Y. Guitton +getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) { + cat("Creating BIC pdf...\n") + + if (is.null(xcmsSet)) { + cat("Enter an xcmsSet \n") + stop() + } else { + files <- filepaths(xcmsSet) + } + + 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[,"class"]==phenoDataClass[i]) + } + + N <- dim(phenoData(xcmsSet))[1] + + TIC <- vector("list",N) + + + for (j in 1:N) { + + TIC[[j]] <- getBPC(files[j]) + #good for raw + # seems strange for corrected + #errors if scanrange used in xcmsSetgeneration + if (!is.null(xcmsSet) && rt == "corrected") + rtcor <- xcmsSet@rt$corrected[[j]] + else + rtcor <- NULL + + TIC[[j]] <- getBPC(files[j],rtcor=rtcor) + # TIC[[j]][,1]<-rtcor + } + + + + pdf(pdfname,w=16,h=10) + cols <- rainbow(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]) + + + ##plot start + + if (length(phenoDataClass)>2){ + 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 + 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]]) + } + 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]]) + } + 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") + + 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]]) + } + 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]]) + } + 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") + + 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]]) + } + + legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch) + + }#end length ==1 + + dev.off() #pdf(pdfname,w=16,h=10) + + invisible(TIC) +} + + + +#@author Y. Guitton +getTIC <- function(file, rtcor=NULL) { + object <- xcmsRaw(file) + cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object, mzrange=range(object@env$mz))$intensity) +} + +#overlay TIC from all files in current folder or from xcmsSet, create pdf +#@author Y. Guitton +getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf", rt=c("raw","corrected")) { + cat("Creating TIC pdf...\n") + + if (is.null(xcmsSet)) { + filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") + filepattern <- paste(paste("\\.", filepattern, "$", sep=""), collapse="|") + if (is.null(files)) + files <- getwd() + info <- file.info(files) + 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[,"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[,"class"]==phenoDataClass[i]) + } + + N <- length(files) + TIC <- vector("list",N) + + for (i in 1:N) { + if (!is.null(xcmsSet) && rt == "corrected") + rtcor <- xcmsSet@rt$corrected[[i]] else + rtcor <- NULL + TIC[[i]] <- getTIC(files[i], rtcor=rtcor) + } + + pdf(pdfname, w=16, h=10) + cols <- rainbow(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]) + + + ##plot start + if (length(phenoDataClass)>2){ + 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 + 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]]) + } + 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]]) + } + 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 + + 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]]) + } + 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]]) + } + 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]))) + + 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]]) + } + + legend("topright",paste(basename(files[c(classnames[[k]])])), col=colvect, lty=lty, pch=pch) + + }#end length ==1 + + dev.off() #pdf(pdfname,w=16,h=10) + + invisible(TIC) +} + + + +# 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(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") { + cat("Creating the sampleMetadata file...\n") + + #Create the sampleMetada dataframe + 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()) + for (sampleName in sampleNamesOrigin) { + write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) + } + stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") + } + + if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { + 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") + for (sampleName in sampleNamesOrigin) { + cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) + } + } + + sampleMetadata$sampleMetadata <- sampleNamesMakeNames + + + #For each sample file, the following actions are done + for (fileIdx in 1:length(fileNames(xdata))) { + #Check if the file is in the CDF format + if (!mzR:::netCDFIsFile(fileNames(xdata))) { + + # If the column isn't exist, with add one filled with NA + if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA + + #Extract the polarity (a list of polarities) + polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"] + #Verify if all the scans have the same polarity + uniq_list <- unique(polarity) + if (length(uniq_list)>1){ + polarity <- "mixed" + } else { + polarity <- as.character(uniq_list) + } + + #Set the polarity attribute + sampleMetadata$polarity[fileIdx] <- polarity + } + + } + + write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) + + return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames)) + +} + + +# This function check if xcms will found all the files +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM +checkFilesCompatibilityWithXcms <- function(directory) { + cat("Checking files filenames compatibilities with xmcs...\n") + # WHAT XCMS WILL FIND + filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") + filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") + info <- file.info(directory) + 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) + files[exists] <- files_abs[exists] + files[exists] <- sub("//","/",files[exists]) + + # WHAT IS ON THE FILESYSTEM + filesystem_filepaths <- system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T) + filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] + + # COMPARISON + if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { + write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) + write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) + stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") + } +} + + +#This function list the compatible files within the directory as xcms did +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM +getMSFiles <- function (directory) { + filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") + filepattern <- paste(paste("\\.", filepattern, "$", 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. +#@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 $xml;fi; done;") + capture <- system(cmd, intern=TRUE) + + if (length(capture)>0){ + #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) + write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr()) + write(capture, stderr()) + stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files") + } + +} + + +# This function check if XML contain special characters +#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM +deleteXmlBadCharacters<- function (directory) { + cat("Checking Non ASCII characters in the XML...\n") + + processed <- F + l <- system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE) + for (i in l){ + cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="") + capture <- suppressWarnings(system(cmd, intern=TRUE)) + if (length(capture)>0){ + cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) + print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") ) + c <- system(cmd, intern=TRUE) + capture <- "" + processed <- T + } + } + if (processed) cat("\n\n") + return(processed) +} + + +# This function will compute MD5 checksum to check the data integrity +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +getMd5sum <- function (directory) { + cat("Compute md5 checksum...\n") + # WHAT XCMS WILL FIND + filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") + filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") + 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] + + library(tools) + + #cat("\n\n") + + return(as.matrix(md5sum(files))) +} + + +# This function get the raw file path from the arguments +#@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(args$singlefile_galaxyPath)) { + singlefile_galaxyPaths <- args$singlefile_galaxyPath; + singlefile_sampleNames <- args$singlefile_sampleName + } + if (!is.null(args$singlefile_galaxyPathPositive)) { + singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive; + singlefile_sampleNames <- args$singlefile_sampleNamePositive + } + 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 <- 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 + } + } + for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) { + args[[argument]] <- NULL + } + 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]] + 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!") + print(error_message); stop(error_message) + } + + if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T))) + file.copy(singlefile_galaxyPath, singlefile_sampleName) + + } + directory <- "." + + } + 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!") + print(error_message) + stop(error_message) + } + + #list all file in the zip file + #zip_files <- unzip(zipfile,list=T)[,"Name"] + + #unzip + suppressWarnings(unzip(zipfile, unzip="unzip")) + + #get the directory name + 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(...) +}