R/PlotCombinedDynamicRange.R

In BioAlvaro/MQmetrics: Quality Control of Protemics Data

#' Dynamic range of all the samples combined
#'
#' @param MQCombined Object list containing all the files from the MaxQuant
#' output. It is the result from using \code{make_MQCombined}.
#' @param show_shade Creates a shade showing where the \code{percent_proteins}
#' are. Default is TRUE.
#' @param percent_proteins Determines the percentage for the show_shade
#' parameter. Default is 0.90 (90\% of the proteins).
#'
#' @return Returns the dynamic range for all samples combined.
#'
#' @export
#'
#' @examples
#' MQPathCombined <- system.file("extdata/combined/", package = "MQmetrics")
#' MQCombined <- make_MQCombined(MQPathCombined)
#' PlotCombinedDynamicRange(MQCombined)
PlotCombinedDynamicRange <- function(MQCombined,
                                    show_shade = TRUE,
                                    percent_proteins = 0.90) {
    proteinGroups <- MQCombined$proteinGroups.txt

    Intensity <- NULL

    rank <- proteinGroups %>% select(c(Intensity))
    rank <- rank[order(rank$Intensity, decreasing = TRUE), ]
    rank$Intensity <- log10(rank$Intensity)

    if (length(grep("-Inf", rank$Intensity)) > 0) {
        rank <- rank[-grep("-Inf", rank$Intensity), ]
    }

    vector1 <- seq_len(nrow(rank))
    # Plot error bar to include the 90% of the proteins, 5% on left side,
    # 5% on the right one

    a <- ggplot(rank, aes(x = vector1, y = Intensity)) +
        theme_bw() +
        theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
        ggtitle("Dynamic range") +
        ylab(expression("Log"[10] * "(Intensity)")) +
        xlab("Protein Abundance Rank")

    if (show_shade == TRUE) {
        limits <- (1 - percent_proteins) / 2

        limits_row <- round(nrow(rank) * limits)

        upper_y <- rank$Intensity[limits_row]
        bottom_y <- rank$Intensity[nrow(rank) - limits_row]

        orders_abundance <- paste(
            round(upper_y - bottom_y, digits = 1),
            "orders of abundance"
        )

        a + annotate("rect",
                    xmin = limits_row,
                    xmax = nrow(rank) - limits_row,
                    ymin = bottom_y,
                    ymax = upper_y,
                    alpha = 0.3,
                    fill = '#5B84B1FF'
        ) +
            annotate("text",
                    x = nrow(rank) / 2,
                    y = bottom_y,
                    label = orders_abundance
            ) +
            annotate("text",
                    x = nrow(rank) / 2,
                    y = upper_y,
                    label = paste0(
                    percent_proteins * 100,
                    #" % of proteins represented."
                    " % of proteins"
                    )
            )+
            geom_point(colour = "#FC766AFF", alpha = 0.75, shape = 21)
    } else {
        a +geom_point(colour = "#FC766AFF", alpha = 0.75, shape = 21)
    }
}