mnsbase_readmsdata: lib.r annotate

annotate lib.r @ 0:3f0a218e2ebc draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a

author	lecorguille
date	Tue, 03 Apr 2018 11:45:58 -0400
parents
children

rev	line source
0 3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	3
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	4 #@author G. Le Corguille
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	6 parseCommandArgs <- function(...) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	7 args <- batch::parseCommandArgs(...)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	8 for (key in names(args)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	9 if (args[key] %in% c("TRUE","FALSE"))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	10 args[key] = as.logical(args[key])
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	11 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	12 return(args)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	13 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	14
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	15 #@author G. Le Corguille
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	16 # This function will
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	17 # - load the packages
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	18 # - display the sessionInfo
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	21
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	22 sessioninfo = sessionInfo()
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	23 cat(sessioninfo$R.version$version.string,"\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	24 cat("Main packages:\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	26 cat("Other loaded packages:\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	28 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	29
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	30 #@author G. Le Corguille
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	31 # This function merge several xdata into one.
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	32 mergeXData <- function(args) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	33 for(image in args$images) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	34 load(image)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	35 # Handle infiles
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	36 if (!exists("singlefile")) singlefile <- NULL
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	37 if (!exists("zipfile")) zipfile <- NULL
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	38 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	39 zipfile <- rawFilePath$zipfile
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	40 singlefile <- rawFilePath$singlefile
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	41 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	42 if (exists("raw_data")) xdata <- raw_data
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	43 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	44 cat(sampleNamesList$sampleNamesOrigin,"\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	45 if (!exists("xdata_merged")) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	46 xdata_merged <- xdata
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	47 singlefile_merged <- singlefile
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	48 md5sumList_merged <- md5sumList
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	49 sampleNamesList_merged <- sampleNamesList
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	50 } else {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	51 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	52 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	53 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	54 singlefile_merged <- c(singlefile_merged,singlefile)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	55 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	56 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	57 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	58 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	59 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	60 rm(image)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	61 xdata <- xdata_merged; rm(xdata_merged)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	62 singlefile <- singlefile_merged; rm(singlefile_merged)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	63 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	64 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	65
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	66 if (!is.null(args$sampleMetadata)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	67 cat("\tXSET PHENODATA SETTING...\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	68 sampleMetadataFile <- args$sampleMetadata
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	69 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	70 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	71
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	72 if (any(is.na(pData(xdata)$sample_group))) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	73 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	74 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	75 print(error_message)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	76 stop(error_message)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	77 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	78 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	79 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	80 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	81
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	82 #@author G. Le Corguille
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	83 # This function convert if it is required the Retention Time in minutes
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	84 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	85 if (convertRTMinute){
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	86 #converting the retention times (seconds) into minutes
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	87 print("converting the retention times into minutes in the variableMetadata")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	88 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	89 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	90 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	91 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	92 return (variableMetadata)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	93 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	94
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	95 #@author G. Le Corguille
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	96 # This function format ions identifiers
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	97 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	98 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	99 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	100 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	101 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	102 return(variableMetadata)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	103 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	104
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	105 #@author G. Le Corguille
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	106 # Draw the plotChromPeakDensity 3 per page in a pdf file
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	107 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	108 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	109
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	110 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	111
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	112 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	113 names(group_colors) <- unique(xdata$sample_group)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	114
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	115 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	116 for (i in 1:nrow(featureDefinitions(xdata))) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	117 mzmin = featureDefinitions(xdata)[i,]$mzmin
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	118 mzmax = featureDefinitions(xdata)[i,]$mzmax
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	119 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	120 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	121 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	122
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	123 dev.off()
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	124 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	125
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	126 #@author G. Le Corguille
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	127 # Draw the plotChromPeakDensity 3 per page in a pdf file
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	128 getPlotAdjustedRtime <- function(xdata) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	129
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	130 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	131
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	132 # Color by group
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	133 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	134 if (length(group_colors) > 1) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	135 names(group_colors) <- unique(xdata$sample_group)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	136 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	137 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	138 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	139
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	140 # Color by sample
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	141 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	142 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	143
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	144 dev.off()
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	145 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	146
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	147 #@author G. Le Corguille
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	148 # value: intensity values to be used into, maxo or intb
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	149 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	150 dataMatrix <- featureValues(xdata, method="medret", value=intval)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	151 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	152 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	153 variableMetadata <- featureDefinitions(xdata)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	154 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	155 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	156
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	157 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	158 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	159
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	160 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	161 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	162
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	163 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	164
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	165 #@author G. Le Corguille
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	166 # It allow different of field separators
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	167 getDataFrameFromFile <- function(filename, header=T) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	168 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	169 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	170 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	171 if (ncol(myDataFrame) < 2) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	172 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	173 print(error_message)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	174 stop(error_message)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	175 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	176 return(myDataFrame)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	177 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	178
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	179 getPlotChromatogram <- function(xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	180
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	181 chrom <- chromatogram(xdata, aggregationFun = aggregationFun)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	182 if (aggregationFun == "sum")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	183 type="Total Ion Chromatograms"
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	184 else
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	185 type="Base Peak Intensity Chromatograms"
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	186
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	187 adjusted="Raw"
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	188 if (hasAdjustedRtime(xdata))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	189 adjusted="Adjusted"
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	190
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	191 main <- paste(type,":",adjusted,"data")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	192
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	193 pdf(pdfname, width=16, height=10)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	194
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	195 # Color by group
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	196 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	197 if (length(group_colors) > 1) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	198 names(group_colors) <- unique(xdata$sample_group)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	199 plot(chrom, col = group_colors[chrom$sample_group], main=main)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	200 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	201 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	202
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	203 # Color by sample
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	204 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	205 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	206
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	207 dev.off()
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	208 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	209
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	210 #@author G. Le Corguille
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	211 getPlotTICs <- function(xdata, pdfname="TICs.pdf") {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	212 getPlotChromatogram(xdata, pdfname, aggregationFun = "sum")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	213 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	214
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	215 #@author G. Le Corguille
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	216 getPlotBPIs <- function(xdata, pdfname="BPIs.pdf") {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	217 getPlotChromatogram(xdata, pdfname, aggregationFun = "max")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	218 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	219
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	220
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	221 # Get the polarities from all the samples of a condition
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	222 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	223 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	224 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	225 cat("Creating the sampleMetadata file...\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	226
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	227 #Create the sampleMetada dataframe
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	228 sampleMetadata <- xdata@phenoData@data
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	229 rownames(sampleMetadata) <- NULL
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	230 colnames(sampleMetadata) <- c("sampleMetadata", "class")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	231
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	232 sampleNamesOrigin <- sampleMetadata$sampleMetadata
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	233 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	234
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	235 if (any(duplicated(sampleNamesMakeNames))) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	236 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())
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	237 for (sampleName in sampleNamesOrigin) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	238 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	239 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	240 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	241 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	242
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	243 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	244 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")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	245 for (sampleName in sampleNamesOrigin) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	246 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	247 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	248 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	249
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	250 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	251
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	252
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	253 #For each sample file, the following actions are done
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	254 for (fileIdx in 1:length(fileNames(xdata))) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	255 #Check if the file is in the CDF format
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	256 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	257
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	258 # If the column isn't exist, with add one filled with NA
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	259 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	260
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	261 #Extract the polarity (a list of polarities)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	262 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	263 #Verify if all the scans have the same polarity
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	264 uniq_list <- unique(polarity)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	265 if (length(uniq_list)>1){
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	266 polarity <- "mixed"
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	267 } else {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	268 polarity <- as.character(uniq_list)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	269 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	270
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	271 #Set the polarity attribute
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	272 sampleMetadata$polarity[fileIdx] <- polarity
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	273 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	274
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	275 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	276
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	277 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	278
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	279 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	280
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	281 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	282
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	283
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	284 # This function check if xcms will found all the files
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	285 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	286 checkFilesCompatibilityWithXcms <- function(directory) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	287 cat("Checking files filenames compatibilities with xmcs...\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	288 # WHAT XCMS WILL FIND
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	289 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	290 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	291 info <- file.info(directory)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	292 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	293 files <- c(directory[!info$isdir], listed)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	294 files_abs <- file.path(getwd(), files)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	295 exists <- file.exists(files_abs)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	296 files[exists] <- files_abs[exists]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	297 files[exists] <- sub("//","/",files[exists])
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	298
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	299 # WHAT IS ON THE FILESYSTEM
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	300 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.' -not -path 'conda-env' -type f -name \"\""), intern=T)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	301 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	302
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	303 # COMPARISON
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	304 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	305 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	306 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	307 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	308 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	309 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	310
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	311
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	312 #This function list the compatible files within the directory as xcms did
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	313 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	314 getMSFiles <- function (directory) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	315 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	316 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	317 info <- file.info(directory)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	318 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	319 files <- c(directory[!info$isdir], listed)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	320 exists <- file.exists(files)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	321 files <- files[exists]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	322 return(files)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	323 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	324
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	325 # This function check if XML contains special caracters. It also checks integrity and completness.
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	326 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	327 checkXmlStructure <- function (directory) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	328 cat("Checking XML structure...\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	329
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	330 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;")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	331 capture <- system(cmd, intern=TRUE)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	332
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	333 if (length(capture)>0){
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	334 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	335 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	336 write(capture, stderr())
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	337 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	338 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	339
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	340 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	341
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	342
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	343 # This function check if XML contain special characters
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	344 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	345 deleteXmlBadCharacters<- function (directory) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	346 cat("Checking Non ASCII characters in the XML...\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	347
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	348 processed <- F
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	349 l <- system( paste0("find '",directory, "' -not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'"), intern=TRUE)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	350 for (i in l){
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	351 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	352 capture <- suppressWarnings(system(cmd, intern=TRUE))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	353 if (length(capture)>0){
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	354 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	355 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	356 c <- system(cmd, intern=TRUE)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	357 capture <- ""
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	358 processed <- T
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	359 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	360 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	361 if (processed) cat("\n\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	362 return(processed)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	363 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	364
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	365
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	366 # This function will compute MD5 checksum to check the data integrity
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	367 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	368 getMd5sum <- function (directory) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	369 cat("Compute md5 checksum...\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	370 # WHAT XCMS WILL FIND
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	371 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	372 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	373 info <- file.info(directory)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	374 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	375 files <- c(directory[!info$isdir], listed)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	376 exists <- file.exists(files)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	377 files <- files[exists]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	378
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	379 library(tools)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	380
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	381 #cat("\n\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	382
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	383 return(as.matrix(md5sum(files)))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	384 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	385
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	386
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	387 # This function get the raw file path from the arguments
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	388 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	389 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	390 if (!is.null(args$zipfile)) zipfile <- args$zipfile
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	391 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	392 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	393
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	394 if (!is.null(args$singlefile_galaxyPath)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	395 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	396 singlefile_sampleNames <- args$singlefile_sampleName
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	397 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	398 if (!is.null(args$singlefile_galaxyPathPositive)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	399 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	400 singlefile_sampleNames <- args$singlefile_sampleNamePositive
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	401 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	402 if (!is.null(args$singlefile_galaxyPathNegative)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	403 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	404 singlefile_sampleNames <- args$singlefile_sampleNameNegative
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	405 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	406 if (exists("singlefile_galaxyPaths")){
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	407 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\\|"))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	408 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\\|"))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	409
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	410 singlefile <- NULL
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	411 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	412 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	413 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	414 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	415 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	416 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	417 return(list(zipfile=zipfile, singlefile=singlefile))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	418 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	419
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	420
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	421 # This function retrieve the raw file in the working directory
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	422 # - if zipfile: unzip the file with its directory tree
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	423 # - if singlefiles: set symlink with the good filename
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	424 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	425 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	426 if(!is.null(singlefile) && (length("singlefile")>0)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	427 for (singlefile_sampleName in names(singlefile)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	428 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	429 if(!file.exists(singlefile_galaxyPath)){
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	430 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	431 print(error_message); stop(error_message)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	432 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	433
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	434 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	435 file.copy(singlefile_galaxyPath, singlefile_sampleName)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	436
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	437 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	438 directory <- "."
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	439
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	440 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	441 if(!is.null(zipfile) && (zipfile != "")) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	442 if(!file.exists(zipfile)){
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	443 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	444 print(error_message)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	445 stop(error_message)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	446 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	447
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	448 #list all file in the zip file
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	449 #zip_files <- unzip(zipfile,list=T)[,"Name"]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	450
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	451 #unzip
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	452 suppressWarnings(unzip(zipfile, unzip="unzip"))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	453
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	454 #get the directory name
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	455 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	456 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	457 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	458 directory <- "."
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	459 if (length(directories) == 1) directory <- directories
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	460
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	461 cat("files_root_directory\t",directory,"\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	462
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	463 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	464 return (directory)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	465 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	466
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	467
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	468 # This function retrieve a xset like object
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	469 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	470 getxcmsSetObject <- function(xobject) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	471 # XCMS 1.x
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	472 if (class(xobject) == "xcmsSet")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	473 return (xobject)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	474 # XCMS 3.x
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	475 if (class(xobject) == "XCMSnExp") {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	476 # Get the legacy xcmsSet object
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	477 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	478 sampclass(xset) <- xset@phenoData$sample_group
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	479 return (xset)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	480 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	481 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	482
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	483
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	484 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	485 # https://github.com/sneumann/xcms/issues/250
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	486 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	487 mzfmt <- paste("%.", mzdec, "f", sep = "")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	488 rtfmt <- paste("%.", rtdec, "f", sep = "")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	489
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	490 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	491 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	492
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	493 if (any(dup <- duplicated(gnames)))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	494 for (dupname in unique(gnames[dup])) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	495 dupidx <- which(gnames == dupname)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	496 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	497 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	498
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	499 return (gnames)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	500 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	501
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	502 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	503 # https://github.com/sneumann/xcms/issues/247
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	504 .concatenate_XCMSnExp <- function(...) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	505 x <- list(...)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	506 if (length(x) == 0)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	507 return(NULL)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	508 if (length(x) == 1)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	509 return(x[[1]])
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	510 ## Check that all are XCMSnExp objects.
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	511 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	512 stop("All passed objects should be 'XCMSnExp' objects")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	513 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	514 ## If any of the XCMSnExp has alignment results or detected features drop
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	515 ## them!
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	516 x <- lapply(x, function(z) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	517 if (hasAdjustedRtime(z)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	518 z <- dropAdjustedRtime(z)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	519 warning("Adjusted retention times found, had to drop them.")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	520 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	521 if (hasFeatures(z)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	522 z <- dropFeatureDefinitions(z)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	523 warning("Feature definitions found, had to drop them.")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	524 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	525 z
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	526 })
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	527 ## Combine peaks
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	528 fls <- lapply(x, fileNames)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	529 startidx <- cumsum(lengths(fls))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	530 pks <- lapply(x, chromPeaks)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	531 procH <- lapply(x, processHistory)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	532 for (i in 2:length(fls)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	533 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	534 procH[[i]] <- lapply(procH[[i]], function(z) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	535 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	536 z
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	537 })
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	538 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	539 pks <- do.call(rbind, pks)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	540 new_x@.processHistory <- unlist(procH)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	541 chromPeaks(new_x) <- pks
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	542 if (validObject(new_x))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	543 new_x
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	544 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	545
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	546 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	547 # https://github.com/sneumann/xcms/issues/247
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	548 .concatenate_OnDiskMSnExp <- function(...) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	549 x <- list(...)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	550 if (length(x) == 0)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	551 return(NULL)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	552 if (length(x) == 1)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	553 return(x[[1]])
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	554 ## Check that all are XCMSnExp objects.
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	555 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	556 stop("All passed objects should be 'OnDiskMSnExp' objects")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	557 ## Check processingQueue
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	558 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	559 new_procQ <- procQ[[1]]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	560 is_ok <- unlist(lapply(procQ, function(z)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	561 !is.character(all.equal(new_procQ, z))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	562 ))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	563 if (any(!is_ok)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	564 warning("Processing queues from the submitted objects differ! ",
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	565 "Dropping the processing queue.")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	566 new_procQ <- list()
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	567 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	568 ## processingData
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	569 fls <- lapply(x, function(z) z@processingData@files)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	570 startidx <- cumsum(lengths(fls))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	571 ## featureData
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	572 featd <- lapply(x, fData)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	573 ## Have to update the file index and the spectrum names.
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	574 for (i in 2:length(featd)) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	575 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	576 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	577 fileIds = featd[[i]]$fileIdx,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	578 spectrumIds = featd[[i]]$spIdx,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	579 nSpectra = nrow(featd[[i]]),
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	580 nFiles = length(unlist(fls))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	581 )
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	582 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	583 featd <- do.call(rbind, featd)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	584 featd$spectrum <- 1:nrow(featd)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	585 ## experimentData
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	586 expdata <- lapply(x, function(z) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	587 ed <- z@experimentData
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	588 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	589 instrumentModel = ed@instrumentModel,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	590 ionSource = ed@ionSource,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	591 analyser = ed@analyser,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	592 detectorType = ed@detectorType,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	593 stringsAsFactors = FALSE)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	594 })
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	595 expdata <- do.call(rbind, expdata)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	596 expdata <- new("MIAPE",
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	597 instrumentManufacturer = expdata$instrumentManufacturer,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	598 instrumentModel = expdata$instrumentModel,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	599 ionSource = expdata$ionSource,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	600 analyser = expdata$analyser,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	601 detectorType = expdata$detectorType)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	602
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	603 ## protocolData
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	604 protodata <- lapply(x, function(z) z@protocolData)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	605 if (any(unlist(lapply(protodata, nrow)) > 0))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	606 warning("Found non-empty protocol data, but merging protocol data is",
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	607 " currently not supported. Skipped.")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	608 ## phenoData
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	609 pdata <- do.call(rbind, lapply(x, pData))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	610 res <- new(
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	611 "OnDiskMSnExp",
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	612 phenoData = new("NAnnotatedDataFrame", data = pdata),
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	613 featureData = new("AnnotatedDataFrame", featd),
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	614 processingData = new("MSnProcess",
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	615 processing = paste0("Concatenated [", date(), "]"),
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	616 files = unlist(fls), smoothed = NA),
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	617 experimentData = expdata,
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	618 spectraProcessingQueue = new_procQ)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	619 if (validObject(res))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	620 res
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	621 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	622
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	623 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	624 # https://github.com/sneumann/xcms/issues/247
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	625 c.XCMSnExp <- function(...) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	626 .concatenate_XCMSnExp(...)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	627 }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	628
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	629 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	630 # https://github.com/sneumann/xcms/issues/247
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	631 c.MSnbase <- function(...) {
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	632 .concatenate_OnDiskMSnExp(...)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a lecorguille parents: diff changeset	633 }

Mercurial > repos > lecorguille > mnsbase_readmsdata

annotate lib.r @ 0:3f0a218e2ebc draft default tip