comparison lib.r @ 5:7c0cc7a3c3db draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639

4:caf45efb34bf

    return (dataMatrix)
}

#@author G. Le Corguille
# Draw the plotChromPeakDensity 3 per page in a pdf file
getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
    pdf(file="plotChromPeakDensity.pdf", width=16, height=12)

    par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))

    group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]

    xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
    for (i in 1:nrow(featureDefinitions(xdata))) {
        mzmin = featureDefinitions(xdata)[i,]$mzmin
        mzmax = featureDefinitions(xdata)[i,]$mzmax
        plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
    }

    dev.off()
}

#@author G. Le Corguille
# value: intensity values to be used into, maxo or intb
getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
    dataMatrix <- featureValues(xdata, method="medret", value=intval)
    colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
    dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
    variableMetadata <- featureDefinitions(xdata)
    colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
    variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)

    variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
    variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
    dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)

5:7c0cc7a3c3db

    return (dataMatrix)
}

#@author G. Le Corguille
# Draw the plotChromPeakDensity 3 per page in a pdf file
getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) {
    pdf(file="plotChromPeakDensity.pdf", width=16, height=12)

    par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))

    group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]

    xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
    for (i in 1:nrow(featureDefinitions(xdata))) {
        mzmin = featureDefinitions(xdata)[i,]$mzmin
        mzmax = featureDefinitions(xdata)[i,]$mzmax
        plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
        legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
    }

    dev.off()
}

#@author G. Le Corguille
# value: intensity values to be used into, maxo or intb
getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
    dataMatrix <- featureValues(xdata, method="medret", value=intval)
    colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
    dataMatrix = cbind(name=groupnames(xdata), dataMatrix)
    variableMetadata <- featureDefinitions(xdata)
    colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
    variableMetadata = data.frame(name=groupnames(xdata), variableMetadata)

    variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
    variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
    dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)