xcms_refine: lib.r annotate

annotate lib.r @ 0:eb115eb8f25c draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"

author	workflow4metabolomics
date	Thu, 17 Jun 2021 07:42:55 +0000
parents
children	20f8ebc3a391

rev	line source
0 eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	3
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	4 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	6 parseCommandArgs <- function(...) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	7 args <- batch::parseCommandArgs(...)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	8 for (key in names(args)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	9 if (args[key] %in% c("TRUE", "FALSE"))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	10 args[key] <- as.logical(args[key])
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	11 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	12 return(args)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	13 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	14
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	15 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	16 # This function will
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	17 # - load the packages
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	18 # - display the sessionInfo
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	20 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	21
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	22 sessioninfo <- sessionInfo()
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	23 cat(sessioninfo$R.version$version.string, "\n")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	24 cat("Main packages:\n")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	26 cat(paste(pkg, packageVersion(pkg)), "\t")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	27 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	28 cat("\n")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	29 cat("Other loaded packages:\n")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	30 for (pkg in names(sessioninfo$loadedOnly)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	31 cat(paste(pkg, packageVersion(pkg)), "\t")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	32 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	33 cat("\n")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	34 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	35
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	36 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	37 # This function merge several chromBPI or chromTIC into one.
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	38 mergeChrom <- function(chrom_merged, chrom) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	39 if (is.null(chrom_merged)) return(NULL)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	40 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	41 return(chrom_merged)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	42 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	43
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	44 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	45 # This function merge several xdata into one.
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	46 mergeXData <- function(args) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	47 chromTIC <- NULL
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	48 chromBPI <- NULL
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	49 chromTIC_adjusted <- NULL
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	50 chromBPI_adjusted <- NULL
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	51 md5sumList <- NULL
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	52 for (image in args$images) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	53
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	54 load(image)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	55 # Handle infiles
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	56 if (!exists("singlefile")) singlefile <- NULL
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	57 if (!exists("zipfile")) zipfile <- NULL
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	59 zipfile <- rawFilePath$zipfile
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	60 singlefile <- rawFilePath$singlefile
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	61
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	62 if (exists("raw_data")) xdata <- raw_data
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	63 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	64
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	65 cat(sampleNamesList$sampleNamesOrigin, "\n")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	66
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	67 if (!exists("xdata_merged")) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	68 xdata_merged <- xdata
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	69 singlefile_merged <- singlefile
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	70 md5sumList_merged <- md5sumList
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	71 sampleNamesList_merged <- sampleNamesList
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	72 chromTIC_merged <- chromTIC
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	73 chromBPI_merged <- chromBPI
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	74 chromTIC_adjusted_merged <- chromTIC_adjusted
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	75 chromBPI_adjusted_merged <- chromBPI_adjusted
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	76 } else {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	77 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	78 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	79 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	80
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	81 singlefile_merged <- c(singlefile_merged, singlefile)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	82 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	83 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	84 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	85 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	86 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	87 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	88 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	89 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	90 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	91 rm(image)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	92 xdata <- xdata_merged; rm(xdata_merged)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	93 singlefile <- singlefile_merged; rm(singlefile_merged)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	94 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	95 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	96
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	97 if (!is.null(args$sampleMetadata)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	98 cat("\tXSET PHENODATA SETTING...\n")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	99 sampleMetadataFile <- args$sampleMetadata
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	100 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = F)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	101 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	102
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	103 if (any(is.na(pData(xdata)$sample_group))) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	104 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	105 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " "))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	106 print(error_message)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	107 stop(error_message)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	108 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	109 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	110
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	111 if (!is.null(chromTIC_merged)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	112 chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	113 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	114 if (!is.null(chromBPI_merged)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	115 chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	116 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	117 if (!is.null(chromTIC_adjusted_merged)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	118 chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	119 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	120 if (!is.null(chromBPI_adjusted_merged)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	121 chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	122 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	123
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	124 return(list("xdata" = xdata, "singlefile" = singlefile, "md5sumList" = md5sumList, "sampleNamesList" = sampleNamesList, "chromTIC" = chromTIC, "chromBPI" = chromBPI, "chromTIC_adjusted" = chromTIC_adjusted, "chromBPI_adjusted" = chromBPI_adjusted))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	125 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	126
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	127 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	128 # This function convert if it is required the Retention Time in minutes
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	129 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	130 if (convertRTMinute) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	131 #converting the retention times (seconds) into minutes
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	132 print("converting the retention times into minutes in the variableMetadata")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	133 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	134 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	135 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	136 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	137 return(variableMetadata)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	138 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	139
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	140 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	141 # This function format ions identifiers
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	142 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	143 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	144 idsDeco <- sapply(splitDeco,
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	145 function(x) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	146 deco <- unlist(x)[2]; if (is.na(deco)) return("") else return(paste0("_", deco))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	147 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	148 )
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	149 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	150 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	151 return(variableMetadata)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	152 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	153
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	154 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	155 # This function convert the remain NA to 0 in the dataMatrix
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	156 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	157 if (naTOzero) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	158 dataMatrix[is.na(dataMatrix)] <- 0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	159 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	160 return(dataMatrix)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	161 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	162
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	163 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	164 # Draw the plotChromPeakDensity 3 per page in a pdf file
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	165 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	166 pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	167
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	168 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	169
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	170 if (length(unique(xdata$sample_group)) < 10) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	171 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	172 }else{
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	173 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	174 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	175 names(group_colors) <- unique(xdata$sample_group)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	176 col_per_samp <- as.character(xdata$sample_group)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	177 for (i in seq_len(length(group_colors))) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	178 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	179 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	180
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	181 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	182 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	183 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	184 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	185 plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	186 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	187 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	188
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	189 dev.off()
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	190 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	191
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	192 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	193 # Draw the plotChromPeakDensity 3 per page in a pdf file
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	194 getPlotAdjustedRtime <- function(xdata) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	195
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	196 pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	197
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	198 # Color by group
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	199 if (length(unique(xdata$sample_group)) < 10) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	200 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	201 } else {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	202 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	203 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	204 if (length(group_colors) > 1) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	205 names(group_colors) <- unique(xdata$sample_group)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	206 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	207 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	208 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	209
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	210 # Color by sample
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	211 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	212 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	213
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	214 dev.off()
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	215 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	216
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	217 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	218 # value: intensity values to be used into, maxo or intb
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	219 getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = F, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	220 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	221 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	222 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	223 variableMetadata <- featureDefinitions(xdata)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	224 colnames(variableMetadata)[1] <- "mz"; colnames(variableMetadata)[4] <- "rt"
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	225 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	226
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	227 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	228 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	229 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	230
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	231 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	232 variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	233
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	234 write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = F, row.names = F)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	235 write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = F, row.names = F)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	236
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	237 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	238
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	239 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	240 # It allow different of field separators
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	241 getDataFrameFromFile <- function(filename, header = T) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	242 myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = F)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	243 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = F)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	244 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = F)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	245 if (ncol(myDataFrame) < 2) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	246 error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	247 print(error_message)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	248 stop(error_message)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	249 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	250 return(myDataFrame)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	251 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	252
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	253 #@author G. Le Corguille
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	254 # Draw the BPI and TIC graphics
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	255 # colored by sample names or class names
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	256 getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	257
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	258 if (aggregationFun == "sum")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	259 type <- "Total Ion Chromatograms"
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	260 else
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	261 type <- "Base Peak Intensity Chromatograms"
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	262
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	263 adjusted <- "Raw"
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	264 if (hasAdjustedRtime(xdata))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	265 adjusted <- "Adjusted"
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	266
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	267 main <- paste(type, ":", adjusted, "data")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	268
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	269 pdf(pdfname, width = 16, height = 10)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	270
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	271 # Color by group
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	272 if (length(unique(xdata$sample_group)) < 10) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	273 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	274 }else{
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	275 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	276 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	277 if (length(group_colors) > 1) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	278 names(group_colors) <- unique(xdata$sample_group)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	279 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	280 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	281 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	282
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	283 # Color by sample
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	284 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	285 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	286
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	287 dev.off()
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	288 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	289
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	290
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	291 # Get the polarities from all the samples of a condition
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	292 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	293 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	294 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	295 cat("Creating the sampleMetadata file...\n")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	296
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	297 #Create the sampleMetada dataframe
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	298 sampleMetadata <- xdata@phenoData@data
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	299 rownames(sampleMetadata) <- NULL
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	300 colnames(sampleMetadata) <- c("sample_name", "class")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	301
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	302 sampleNamesOrigin <- sampleMetadata$sample_name
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	303 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	304
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	305 if (any(duplicated(sampleNamesMakeNames))) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	306 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())
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	307 for (sampleName in sampleNamesOrigin) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	308 write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	309 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	310 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	311 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	312
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	313 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	314 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")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	315 for (sampleName in sampleNamesOrigin) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	316 cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	317 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	318 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	319
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	320 sampleMetadata$sample_name <- sampleNamesMakeNames
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	321
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	322
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	323 #For each sample file, the following actions are done
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	324 for (fileIdx in seq_len(length(fileNames(xdata)))) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	325 #Check if the file is in the CDF format
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	326 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	327
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	328 # If the column isn't exist, with add one filled with NA
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	329 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	330
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	331 #Extract the polarity (a list of polarities)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	332 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	333 #Verify if all the scans have the same polarity
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	334 uniq_list <- unique(polarity)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	335 if (length(uniq_list) > 1) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	336 polarity <- "mixed"
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	337 } else {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	338 polarity <- as.character(uniq_list)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	339 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	340
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	341 #Set the polarity attribute
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	342 sampleMetadata$polarity[fileIdx] <- polarity
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	343 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	344
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	345 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	346
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	347 write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	348
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	349 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	350
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	351 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	352
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	353
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	354 # This function will compute MD5 checksum to check the data integrity
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	355 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	356 getMd5sum <- function(files) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	357 cat("Compute md5 checksum...\n")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	358 library(tools)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	359 return(as.matrix(md5sum(files)))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	360 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	361
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	362 # This function retrieve the raw file in the working directory
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	363 # - if zipfile: unzip the file with its directory tree
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	364 # - if singlefiles: set symlink with the good filename
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	365 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	366 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	367
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	368 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	369
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	370 # single - if the file are passed in the command arguments -> refresh singlefile
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	371 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	372 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\\|"))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	373 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\\|"))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	374
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	375 singlefile <- NULL
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	376 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	377 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	378 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	379 # In case, an url is used to import data within Galaxy
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	380 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	381 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	382 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	383 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	384 # zipfile - if the file are passed in the command arguments -> refresh zipfile
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	385 if (!is.null(args[[paste0("zipfile", prefix)]]))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	386 zipfile <- args[[paste0("zipfile", prefix)]]
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	387
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	388 # single
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	389 if (!is.null(singlefile) && (length("singlefile") > 0)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	390 files <- vector()
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	391 for (singlefile_sampleName in names(singlefile)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	392 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	393 if (!file.exists(singlefile_galaxyPath)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	394 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	395 print(error_message); stop(error_message)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	396 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	397
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	398 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = T)))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	399 file.copy(singlefile_galaxyPath, singlefile_sampleName)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	400 files <- c(files, singlefile_sampleName)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	401 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	402 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	403 # zipfile
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	404 if (!is.null(zipfile) && (zipfile != "")) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	405 if (!file.exists(zipfile)) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	406 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	407 print(error_message)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	408 stop(error_message)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	409 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	410 suppressWarnings(unzip(zipfile, unzip = "unzip"))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	411
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	412 #get the directory name
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	413 suppressWarnings(filesInZip <- unzip(zipfile, list = T))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	414 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	415 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	416 directory <- "."
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	417 if (length(directories) == 1) directory <- directories
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	418
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	419 cat("files_root_directory\t", directory, "\n")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	420
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	421 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	422 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "\|")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	423 info <- file.info(directory)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	424 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	425 files <- c(directory[!info$isdir], listed)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	426 exists <- file.exists(files)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	427 files <- files[exists]
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	428
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	429 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	430 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	431
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	432 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	433
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	434
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	435 # This function retrieve a xset like object
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	436 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	437 getxcmsSetObject <- function(xobject) {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	438 # XCMS 1.x
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	439 if (class(xobject) == "xcmsSet")
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	440 return(xobject)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	441 # XCMS 3.x
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	442 if (class(xobject) == "XCMSnExp") {
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	443 # Get the legacy xcmsSet object
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	444 suppressWarnings(xset <- as(xobject, "xcmsSet"))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	445 if (!is.null(xset@phenoData$sample_group))
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	446 sampclass(xset) <- xset@phenoData$sample_group
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	447 else
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	448 sampclass(xset) <- "."
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	449 return(xset)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	450 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55" workflow4metabolomics parents: diff changeset	451 }

Mercurial > repos > workflow4metabolomics > xcms_refine

annotate lib.r @ 0:eb115eb8f25c draft