comparison lib.r @ 35:2b0a4c7a4a48 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty

34:9714270678a7

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

#@author G. Le Corguille
# This function merge several xdata into one.
mergeXData <- function(args) {
    for(image in args$images) {
        load(image)
        # Handle infiles
        if (!exists("singlefile")) singlefile <- NULL
        if (!exists("zipfile")) zipfile <- NULL

        if (!exists("xdata_merged")) {
            xdata_merged <- xdata
            singlefile_merged <- singlefile
            md5sumList_merged <- md5sumList
            sampleNamesList_merged <- sampleNamesList
        } 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)
        }
    }
    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)
        }
    }
    return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList))
}

#@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(xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {

    chrom <- chromatogram(xdata, aggregationFun = aggregationFun)
    if (aggregationFun == "sum")
        type="Total Ion Chromatograms"
    else
        type="Base Peak Intensity Chromatograms"

    # Color by sample
    plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
    legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)

    dev.off()
}

#@author G. Le Corguille
getPlotTICs <- function(xdata, pdfname="TICs.pdf") {
    getPlotChromatogram(xdata, pdfname, aggregationFun = "sum")
}

#@author G. Le Corguille
getPlotBPIs <- function(xdata, pdfname="BPIs.pdf") {
    getPlotChromatogram(xdata, pdfname, aggregationFun = "max")
}


# Get the polarities from all the samples of a condition
#@author Misharl Monsoor [e-mail] ABiMS TEAM

35:2b0a4c7a4a48

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

#@author G. Le Corguille
# This function merge several chromBPI or chromTIC into one.
mergeChrom <- function(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

        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
        type="Base Peak Intensity Chromatograms"

    # Color by sample
    plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
    legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)

    dev.off()
}


# Get the polarities from all the samples of a condition
#@author Misharl Monsoor [e-mail] ABiMS TEAM