comparison lib.r @ 37:35a20d7c9f33 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8

36:e309e6af6744

    for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
}

#@author G. Le Corguille
# This function merge several chromBPI or chromTIC into one.
mergeChrom <- function(chromTIC_merged, chromTIC, xdata_merged) {
    if (is.null(chromTIC_merged)) return(NULL)
    chromTIC_merged@.Data <- cbind(chromTIC_merged@.Data, chromTIC@.Data)
    chromTIC_merged@phenoData <- xdata_merged@phenoData
    return(chromTIC_merged)
}

#@author G. Le Corguille
# This function merge several xdata into one.
mergeXData <- function(args) {
    chromTIC <- NULL; chromBPI <- NULL
    for(image in args$images) {
        load(image)
        # Handle infiles
        if (!exists("singlefile")) singlefile <- NULL
        if (!exists("zipfile")) zipfile <- NULL
        rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
        zipfile <- rawFilePath$zipfile
        singlefile <- rawFilePath$singlefile
        retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
        if (exists("raw_data")) xdata <- raw_data
        if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
        cat(sampleNamesList$sampleNamesOrigin,"\n")
        if (!exists("xdata_merged")) {
            xdata_merged <- xdata
            singlefile_merged <- singlefile
            md5sumList_merged <- md5sumList
            sampleNamesList_merged <- sampleNamesList
            chromTIC_merged <- chromTIC
            chromBPI_merged <- chromBPI
        } else {
            if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
            else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
            else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
            singlefile_merged <- c(singlefile_merged,singlefile)
            md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
            sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
            sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
            chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC, xdata_merged)
            chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI, xdata_merged)
        }
    }
    rm(image)
    xdata <- xdata_merged; rm(xdata_merged)
    singlefile <- singlefile_merged; rm(singlefile_merged)
    md5sumList <- md5sumList_merged; rm(md5sumList_merged)
    sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
    chromTIC <- chromTIC_merged; rm(chromTIC_merged)
    chromBPI <- chromBPI_merged; rm(chromBPI_merged)

    if (!is.null(args$sampleMetadata)) {
        cat("\tXSET PHENODATA SETTING...\n")
        sampleMetadataFile <- args$sampleMetadata
        sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)

            error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
            print(error_message)
            stop(error_message)
        }
    }
    return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI))
}

#@author G. Le Corguille
# This function convert if it is required the Retention Time in minutes
RTSecondToMinute <- function(variableMetadata, convertRTMinute) {

        stop(error_message)
    }
    return(myDataFrame)
}

getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {

    if (aggregationFun == "sum")
        type="Total Ion Chromatograms"
    else

    singlefile <- NULL
    for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
      singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
      singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
      # In case, an url is used to import data within Galaxy 
      singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
      singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
    }
  }
  return(list(zipfile=zipfile, singlefile=singlefile))

37:35a20d7c9f33

    for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
}

#@author G. Le Corguille
# This function merge several chromBPI or chromTIC into one.
mergeChrom <- function(chrom_merged, chrom) {
    if (is.null(chrom_merged)) return(NULL)
    chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
    return(chrom_merged)
}

#@author G. Le Corguille
# This function merge several xdata into one.
mergeXData <- function(args) {
    chromTIC <- NULL
    chromBPI <- NULL
    chromTIC_adjusted <- NULL
    chromBPI_adjusted <- NULL
    for(image in args$images) {

        load(image)
        # Handle infiles
        if (!exists("singlefile")) singlefile <- NULL
        if (!exists("zipfile")) zipfile <- NULL
        rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
        zipfile <- rawFilePath$zipfile
        singlefile <- rawFilePath$singlefile
        retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)

        if (exists("raw_data")) xdata <- raw_data
        if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")

        cat(sampleNamesList$sampleNamesOrigin,"\n")

        if (!exists("xdata_merged")) {
            xdata_merged <- xdata
            singlefile_merged <- singlefile
            md5sumList_merged <- md5sumList
            sampleNamesList_merged <- sampleNamesList
            chromTIC_merged <- chromTIC
            chromBPI_merged <- chromBPI
            chromTIC_adjusted_merged <- chromTIC_adjusted
            chromBPI_adjusted_merged <- chromBPI_adjusted
        } else {
            if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
            else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
            else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")

            singlefile_merged <- c(singlefile_merged,singlefile)
            md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
            sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
            sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
            chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
            chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
            chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
            chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
        }
    }
    rm(image)
    xdata <- xdata_merged; rm(xdata_merged)
    singlefile <- singlefile_merged; rm(singlefile_merged)
    md5sumList <- md5sumList_merged; rm(md5sumList_merged)
    sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)

    if (!is.null(args$sampleMetadata)) {
        cat("\tXSET PHENODATA SETTING...\n")
        sampleMetadataFile <- args$sampleMetadata
        sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)

            error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
            print(error_message)
            stop(error_message)
        }
    }

    if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
    if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
    if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
    if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }

    return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
}

#@author G. Le Corguille
# This function convert if it is required the Retention Time in minutes
RTSecondToMinute <- function(variableMetadata, convertRTMinute) {

        stop(error_message)
    }
    return(myDataFrame)
}

#@author G. Le Corguille
# Draw the BPI and TIC graphics
# colored by sample names or class names
getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {

    if (aggregationFun == "sum")
        type="Total Ion Chromatograms"
    else

    singlefile <- NULL
    for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
      singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
      singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
      # In case, an url is used to import data within Galaxy
      singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
      singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
    }
  }
  return(list(zipfile=zipfile, singlefile=singlefile))