R/PlotPeaks.R

In BioAlvaro/MQmetrics: Quality Control of Protemics Data

#' Total number of peaks detected and sequenced
#'
#' @param MQCombined Object list containing all the files from the MaxQuant
#' output. It is the result from using \code{make_MQCombined}.
#' @param long_names If TRUE, samples having long names will be considered, and
#'  the name will be split by sep_names. By default = FALSE.
#' @param sep_names If long_names is TRUE, sep_names has to be selected. Samples
#'  names will be split. By default is NULL.
#' @param position_dodge_width Position of the columns within each others.
#' @param palette The palette from the Package RColorBrewer. By default is
#' 'Set2'.
#'
#' @return Plots the total number of peaks detected in the full scans and the
#'  total number of peaks sequenced by tandem MS.
#' @export
#'
#' @examples
#' MQPathCombined <- system.file("extdata/combined/", package = "MQmetrics")
#' MQCombined <- make_MQCombined(MQPathCombined)
#' PlotPeaks(MQCombined)
PlotPeaks <- function(MQCombined,
                    long_names = FALSE,
                    sep_names = NULL,
                    position_dodge_width = 1,
                    palette = "Set2") {

    summary <- MQCombined$summary.txt

    Experiment <- `Peaks Sequenced` <- Peaks <- value <- variable <- NULL
    `Peaks sequenced` <- NULL

    MaxQuant_version <- MQCombined$parameters$Value[
        MQCombined$parameters$Parameter == 'Version']

    #Detect MaxQuant Version to read column names accordingly.

    if (base::startsWith(MaxQuant_version, '1')) {

        a <- summary %>% select(c(Experiment, Peaks, `Peaks Sequenced`))
    } else{
        a <- summary %>% select(c(Experiment, Peaks, `Peaks sequenced`))

    }

    a_melt <- melt(a, id.vars = "Experiment")

    b <- ggplot(a_melt, aes(
        x = Experiment,
        y = value,
        group = variable,
        fill = variable)
        ) +
        geom_bar(
            stat = "identity",
            colour = "black",
            position = position_dodge(width = position_dodge_width)
        ) +
        theme_bw() +
        ylab("Number of Peaks") +
        ggtitle("Peaks detected and sequenced in the full scans") +
        scale_fill_brewer(palette = palette) +
        theme(legend.position = "bottom")+
        labs(fill = element_blank())


    if (long_names == TRUE) {
        b + scale_x_discrete(labels = function(x) {
                stringr::str_wrap(gsub(sep_names," ", x),3)})
    } else {
        b
    }
}