Mercurial > repos > lecorguille > xcms_retcor
view lib.r @ 21:7faadba7c625 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
author | lecorguille |
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date | Tue, 30 Apr 2019 04:45:06 -0400 |
parents | 9784ec912994 |
children | 972e76582173 |
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#@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 merge several chromBPI or chromTIC into one. mergeChrom <- function(chrom_merged, chrom) { if (is.null(chrom_merged)) return(NULL) chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data) return(chrom_merged) } #@author G. Le Corguille # This function merge several xdata into one. mergeXData <- function(args) { chromTIC <- NULL chromBPI <- NULL chromTIC_adjusted <- NULL chromBPI_adjusted <- NULL for(image in args$images) { load(image) # Handle infiles if (!exists("singlefile")) singlefile <- NULL if (!exists("zipfile")) zipfile <- NULL rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) zipfile <- rawFilePath$zipfile singlefile <- rawFilePath$singlefile retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) if (exists("raw_data")) xdata <- raw_data if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") cat(sampleNamesList$sampleNamesOrigin,"\n") if (!exists("xdata_merged")) { xdata_merged <- xdata singlefile_merged <- singlefile md5sumList_merged <- md5sumList sampleNamesList_merged <- sampleNamesList chromTIC_merged <- chromTIC chromBPI_merged <- chromBPI chromTIC_adjusted_merged <- chromTIC_adjusted chromBPI_adjusted_merged <- chromBPI_adjusted } else { if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata) else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata) else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") singlefile_merged <- c(singlefile_merged,singlefile) md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin) sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin) sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames) chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC) chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI) chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted) chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted) } } rm(image) xdata <- xdata_merged; rm(xdata_merged) singlefile <- singlefile_merged; rm(singlefile_merged) md5sumList <- md5sumList_merged; rm(md5sumList_merged) sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged) if (!is.null(args$sampleMetadata)) { cat("\tXSET PHENODATA SETTING...\n") sampleMetadataFile <- args$sampleMetadata sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F) xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)] if (any(is.na(pData(xdata)$sample_group))) { sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)] error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" ")) print(error_message) stop(error_message) } } if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData } if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData } if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData } if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData } return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted)) } #@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 # This function convert the remain NA to 0 in the dataMatrix naTOzeroDataMatrix <- function(dataMatrix, naTOzero) { if (naTOzero){ dataMatrix[is.na(dataMatrix)] <- 0 } return (dataMatrix) } #@author G. Le Corguille # Draw the plotChromPeakDensity 3 per page in a pdf file getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) { 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))) { mzmin = featureDefinitions(xdata)[i,]$mzmin mzmax = featureDefinitions(xdata)[i,]$mzmax plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) 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$sample_group))] if (length(group_colors) > 1) { names(group_colors) <- unique(xdata$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, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) { dataMatrix <- featureValues(xdata, method="medret", value=intval) colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix))) dataMatrix = cbind(name=groupnames(xdata), dataMatrix) variableMetadata <- featureDefinitions(xdata) colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" variableMetadata = data.frame(name=groupnames(xdata), variableMetadata) variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero) # FIX: issue when the vector at peakidx is too long and is written in a new line during the export variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",") 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 G. Le Corguille # It allow different of field separators getDataFrameFromFile <- function(filename, header=T) { myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F) if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F) if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F) if (ncol(myDataFrame) < 2) { error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation" print(error_message) stop(error_message) } return(myDataFrame) } #@author G. Le Corguille # Draw the BPI and TIC graphics # colored by sample names or class names getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") { if (aggregationFun == "sum") type="Total Ion Chromatograms" else type="Base Peak Intensity Chromatograms" adjusted="Raw" if (hasAdjustedRtime(xdata)) adjusted="Adjusted" main <- paste(type,":",adjusted,"data") pdf(pdfname, width=16, height=10) # Color by group group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] if (length(group_colors) > 1) { names(group_colors) <- unique(xdata$sample_group) plot(chrom, col = group_colors[chrom$sample_group], main=main) legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) } # Color by sample plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main) legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1) dev.off() } # 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("sample_name", "class") sampleNamesOrigin <- sampleMetadata$sample_name sampleNamesMakeNames <- make.names(sampleNamesOrigin) if (any(duplicated(sampleNamesMakeNames))) { write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr()) for (sampleName in sampleNamesOrigin) { write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) } stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") } if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n") for (sampleName in sampleNamesOrigin) { cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) } } sampleMetadata$sample_name <- 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$isdir], listed) files_abs <- file.path(getwd(), files) exists <- file.exists(files_abs) files[exists] <- files_abs[exists] files[exists] <- sub("//","/",files[exists]) # WHAT IS ON THE FILESYSTEM filesystem_filepaths <- system(paste0("find \"",getwd(),"/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] # COMPARISON if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") } } #This function list the compatible files within the directory as xcms did #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM getMSFiles <- function (directory) { filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") filepattern <- paste(paste("\\.", filepattern, "$", 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 <- 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 $xml;fi; done;") capture <- system(cmd, intern=TRUE) if (length(capture)>0){ #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr()) write(capture, stderr()) stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files") } } # This function check if XML contain special characters #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM deleteXmlBadCharacters<- function (directory) { cat("Checking Non ASCII characters in the XML...\n") processed <- F l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE) for (i in l){ cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="") capture <- suppressWarnings(system(cmd, intern=TRUE)) if (length(capture)>0){ cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") ) c <- system(cmd, intern=TRUE) capture <- "" processed <- T } } if (processed) cat("\n\n") return(processed) } # This function will compute MD5 checksum to check the data integrity #@author Gildas Le Corguille lecorguille@sb-roscoff.fr getMd5sum <- function (directory) { cat("Compute md5 checksum...\n") # WHAT XCMS WILL FIND filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") filepattern <- paste(paste("\\.", filepattern, "$", 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, prefix="") { if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'") if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]] if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) { singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]] singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]] } 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] # In case, an url is used to import data within Galaxy singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1) singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath } } return(list(zipfile=zipfile, singlefile=singlefile)) } # 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')) if (!is.null(xset@phenoData$sample_group)) sampclass(xset) <- xset@phenoData$sample_group else sampclass(xset) <- "." return (xset) } }