annotate lib.r @ 25:aa252eec9229 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"

#@authors ABiMS TEAM, Y. Guitton
# lib.r for Galaxy Workflow4Metabolomics xcms tools

#@author G. Le Corguille
# solve an issue with batch if arguments are logical TRUE/FALSE
parseCommandArgs <- function(...) {
    args <- batch::parseCommandArgs(...)
    for (key in names(args)) {
        if (args[key] %in% c("TRUE", "FALSE"))
            args[key] <- as.logical(args[key])
    }
    return(args)
}

#@author G. Le Corguille
# This function will
# - load the packages
# - display the sessionInfo
loadAndDisplayPackages <- function(pkgs) {
    for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))

    sessioninfo <- sessionInfo()
    cat(sessioninfo$R.version$version.string, "\n")
    cat("Main packages:\n")
    for (pkg in names(sessioninfo$otherPkgs)) {
      cat(paste(pkg, packageVersion(pkg)), "\t")
    }
    cat("\n")
    cat("Other loaded packages:\n")
    for (pkg in names(sessioninfo$loadedOnly)) {
      cat(paste(pkg, packageVersion(pkg)), "\t")
    }
    cat("\n")
}

#@author G. Le Corguille
# This function merge several chromBPI or chromTIC into one.
mergeChrom <- function(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
    md5sumList <- NULL
    for (image in args$images) {

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

        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 <- xcms:::.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)
        xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]

        if (any(is.na(pData(xdata)$sample_group))) {
            sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
            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) {
    if (convertRTMinute) {
        #converting the retention times (seconds) into minutes
        print("converting the retention times into minutes in the variableMetadata")
        variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
        variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
        variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
    }
    return(variableMetadata)
}

#@author G. Le Corguille
# This function format ions identifiers
formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
    splitDeco <- strsplit(as.character(variableMetadata$name), "_")
    idsDeco <- sapply(splitDeco,
      function(x) {
        deco <- unlist(x)[2]; if (is.na(deco)) return("") else return(paste0("_", deco))
      }
    )
    namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
    variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
    return(variableMetadata)
}

#@author G. Le Corguille
# This function convert the remain NA to 0 in the dataMatrix
naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
    if (naTOzero) {
        dataMatrix[is.na(dataMatrix)] <- 0
    }
    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))

    if (length(unique(xdata$sample_group)) < 10) {
        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
    }else{
        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
    }
    names(group_colors) <- unique(xdata$sample_group)
    col_per_samp <- as.character(xdata$sample_group)
    for (i in seq_len(length(group_colors))) {
      col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
    }

    xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
    for (i in seq_len(nrow(featureDefinitions(xdata)))) {
        mzmin <- featureDefinitions(xdata)[i, ]$mzmin
        mzmax <- featureDefinitions(xdata)[i, ]$mzmax
        plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, 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
# Draw the plotChromPeakDensity 3 per page in a pdf file
getPlotAdjustedRtime <- function(xdata) {

    pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)

    # Color by group
    if (length(unique(xdata$sample_group)) < 10) {
        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
    } else {
        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
    }
    if (length(group_colors) > 1) {
        names(group_colors) <- unique(xdata$sample_group)
        plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
        legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
    }

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

    dev.off()
}

#@author G. Le Corguille
# 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)

    # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
    variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")

    write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = F, row.names = F)
    write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = F, row.names = F)

}

#@author G. Le Corguille
# It allow different of field separators
getDataFrameFromFile <- function(filename, header = T) {
    myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = F)
    if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = F)
    if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = F)
    if (ncol(myDataFrame) < 2) {
        error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
        print(error_message)
        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
        type <- "Base Peak Intensity Chromatograms"

    adjusted <- "Raw"
    if (hasAdjustedRtime(xdata))
        adjusted <- "Adjusted"

    main <- paste(type, ":", adjusted, "data")

    pdf(pdfname, width = 16, height = 10)

    # Color by group
    if (length(unique(xdata$sample_group)) < 10) {
        group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
    }else{
        group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
    }
    if (length(group_colors) > 1) {
        names(group_colors) <- unique(xdata$sample_group)
        plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
        legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
    }

    # Color by sample
    plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
    legend("topright", legend = xdata@phenoData@data$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
#@author Gildas Le Corguille [e-mail] ABiMS TEAM
getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
    cat("Creating the sampleMetadata file...\n")

    #Create the sampleMetada dataframe
    sampleMetadata <- xdata@phenoData@data
    rownames(sampleMetadata) <- NULL
    colnames(sampleMetadata) <-  c("sample_name", "class")

    sampleNamesOrigin <- sampleMetadata$sample_name
    sampleNamesMakeNames <- make.names(sampleNamesOrigin)

    if (any(duplicated(sampleNamesMakeNames))) {
        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())
        for (sampleName in sampleNamesOrigin) {
            write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
        }
        stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
    }

    if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
        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")
        for (sampleName in sampleNamesOrigin) {
            cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
        }
    }

    sampleMetadata$sample_name <- sampleNamesMakeNames


    #For each sample file, the following actions are done
    for (fileIdx in seq_len(length(fileNames(xdata)))) {
        #Check if the file is in the CDF format
        if (!mzR:::netCDFIsFile(fileNames(xdata))) {

            # If the column isn't exist, with add one filled with NA
            if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA

            #Extract the polarity (a list of polarities)
            polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
            #Verify if all the scans have the same polarity
            uniq_list <- unique(polarity)
            if (length(uniq_list) > 1) {
                polarity <- "mixed"
            } else {
                polarity <- as.character(uniq_list)
            }

            #Set the polarity attribute
            sampleMetadata$polarity[fileIdx] <- polarity
        }

    }

    write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)

    return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))

}


# This function will compute MD5 checksum to check the data integrity
#@author Gildas Le Corguille [e-mail]
getMd5sum <- function(files) {
    cat("Compute md5 checksum...\n")
    library(tools)
    return(as.matrix(md5sum(files)))
}

# This function retrieve the raw file in the working directory
#   - if zipfile: unzip the file with its directory tree
#   - if singlefiles: set symlink with the good filename
#@author Gildas Le Corguille [e-mail]
retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {

    if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")

    # single - if the file are passed in the command arguments -> refresh singlefile
    if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
      singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
      singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))

      singlefile <- NULL
      for (singlefile_galaxyPath_i in seq_len(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
      }
    }
    # zipfile - if the file are passed in the command arguments -> refresh zipfile
    if (!is.null(args[[paste0("zipfile", prefix)]]))
      zipfile <- args[[paste0("zipfile", prefix)]]

    # single
    if (!is.null(singlefile) && (length("singlefile") > 0)) {
        files <- vector()
        for (singlefile_sampleName in names(singlefile)) {
            singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
            if (!file.exists(singlefile_galaxyPath)) {
                error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
                print(error_message); stop(error_message)
            }

            if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = T)))
                file.copy(singlefile_galaxyPath, singlefile_sampleName)
            files <- c(files, singlefile_sampleName)
        }
    }
    # zipfile
    if (!is.null(zipfile) && (zipfile != "")) {
        if (!file.exists(zipfile)) {
            error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
            print(error_message)
            stop(error_message)
        }
        suppressWarnings(unzip(zipfile, unzip = "unzip"))

        #get the directory name
        suppressWarnings(filesInZip <- unzip(zipfile, list = T))
        directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
        directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
        directory <- "."
        if (length(directories) == 1) directory <- directories

        cat("files_root_directory\t", directory, "\n")

        filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
        filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
        info <- file.info(directory)
        listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
        files <- c(directory[!info$isdir], listed)
        exists <- file.exists(files)
        files <- files[exists]

    }
    return(list(zipfile = zipfile, singlefile = singlefile, files = files))

}


# This function retrieve a xset like object
#@author Gildas Le Corguille [e-mail]
getxcmsSetObject <- function(xobject) {
    # XCMS 1.x
    if (class(xobject) == "xcmsSet")
        return(xobject)
    # XCMS 3.x
    if (class(xobject) == "XCMSnExp") {
        # Get the legacy xcmsSet object
        suppressWarnings(xset <- as(xobject, "xcmsSet"))
        if (!is.null(xset@phenoData$sample_group))
            sampclass(xset) <- xset@phenoData$sample_group
        else
            sampclass(xset) <- "."
        return(xset)
    }
}