R/analysisInfo.R

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

#' AnalysisInfo data.frame methods
#'
#' Various parsing and plotting functions for the analysisInfo data.frame.
#'
#' @param obj,x An \code{analysisInfo} data.frame object as obtained by \link[patRoon]{generateAnalysisInfo} function.
#' @param MSLevel Integer vector with the ms levels (i.e., 1 for MS1 and 2 for MS2) 
#' to obtain traces.
#' @param retentionRange Range of retention time (in seconds), m/z, respectively. Should be a numeric vector with 
#' length of two containing the min/max values. The maximum can be Inf to specify no maximum range. Set to NULL to skip 
#' this step.
#'
#' @name analysisinfo-dataframe
NULL

#' @describeIn analysisinfo-dataframe Obtain the total ion chromatogram/s (TICs) of the analyses.
#' @author Ricardo Cunha, \email{cunha@@iuta.de}
#' @aliases getTICs
#' @export
setMethod("getTICs", "data.frame", function(obj, retentionRange = NULL, MSLevel = 1)
{
    ac <- checkmate::makeAssertCollection()
    checkmate::assertIntegerish(MSLevel, min.len = 1, lower = 1, add = ac)
    obj <- assertAndPrepareAnaInfo(obj, add = ac)
    checkmate::reportAssertions(ac)
    
    filePaths <- getMzMLOrMzXMLAnalysisPath(obj$analysis, obj$path, mustExist = TRUE)
    
    res <- lapply(filePaths, function(fpath)
    {
        hd <- getHeaders(fpath, retentionRange, MSLevel)
        data.table("ret" = hd$retentionTime, "MSLevel" = hd$msLevel, "intensity" = hd$totIonCurrent)
    })
    
    names(res) <- obj$analysis
    res <- rbindlist(res, idcol = "analysis")
    
    if (nrow(res) > 0)
    {
        group <- obj$group
        names(group) <- obj$analysis
        res$group <- group[res$analysis]
        setcolorder(res, c("analysis", "group"))
    }
    
    return(res)
})

#' @describeIn analysisinfo-dataframe Obtain the base peak chromatogram/s (BPCs) of the analyses.
#' @author Ricardo Cunha, \email{cunha@@iuta.de}
#' @aliases getBPCs
#' @export
setMethod("getBPCs", "data.frame", function(obj, retentionRange = NULL, MSLevel = 1)
{
    ac <- checkmate::makeAssertCollection()
    checkmate::assertIntegerish(MSLevel, min.len = 1, lower = 1, add = ac)
    obj <- assertAndPrepareAnaInfo(obj, add = ac)
    checkmate::reportAssertions(ac)
    
    filePaths <- getMzMLOrMzXMLAnalysisPath(obj$analysis, obj$path, mustExist = TRUE)
    
    res <- lapply(filePaths, function(fpath)
    {
        hd <- getHeaders(fpath, retentionRange, MSLevel)
        data.table("ret" = hd$retentionTime, "MSLevel" = hd$msLevel, "mz" = hd$basePeakMZ, "intensity" = hd$basePeakIntensity)
    })
    
    names(res) <- obj$analysis
    res <- rbindlist(res, idcol = "analysis")
    
    if (nrow(res) > 0)
    {
        group <- obj$group
        names(group) <- obj$analysis
        res$group <- group[res$analysis]
        setcolorder(res, c("analysis", "group"))
    }
    
    return(res)
})

#' @describeIn analysisinfo-dataframe Plots the TICs of the analyses.
#' @param retMin Plot retention time in minutes (instead of seconds).
#' @param title Character string used for title of the plot. If \code{NULL} a title will be automatically generated.
#' @param colourBy Sets the automatic colour selection: "none" for a single 
#' colour or "analyses"/"rGroups" for a distinct colour per analysis or analysis replicate group.
#' @param showLegend Plot a legend if TRUE.
#' @template plot-lim
#' @author Ricardo Cunha, \email{cunha@@iuta.de}
#' @aliases plotTICs
#' @export
setMethod("plotTICs", "data.frame", function(obj, retentionRange = NULL, MSLevel = 1, retMin = FALSE, title = NULL, 
                                           colourBy = c("none", "analyses", "rGroups"), showLegend = TRUE, xlim = NULL, 
                                           ylim = NULL, ...)
{
    doPlotHeaders(obj, what = "tic", retentionRange, MSLevel, retMin, title, colourBy, showLegend, xlim, ylim, ...)
})


#' @describeIn analysisinfo-dataframe Plots the BPCs of the analyses.
#' @author Ricardo Cunha, \email{cunha@@iuta.de}
#' @aliases plotBPCs
#' @export
setMethod("plotBPCs", "data.frame", function(obj, retentionRange = NULL, MSLevel = 1, retMin = FALSE, title = NULL,
                                           colourBy = c("none", "analyses", "rGroups"), showLegend = TRUE, xlim = NULL, 
                                           ylim = NULL, ...)
{
    doPlotHeaders(obj, what = "bpc", retentionRange, MSLevel, retMin, title, colourBy, showLegend, xlim, ylim, ...)
})