R/PlotProteaseSpecificity.R

In BioAlvaro/MQmetrics: Quality Control of Protemics Data

#' Protease Specificity
#'
#' @param MQCombined Object list containing all the files from the MaxQuant
#' output. It is the result from using \code{make_MQCombined}.
#' @param palette The palette from the Package RColorBrewer. By default is
#' 'Set2'.
#' @param plots_per_page Establish the maximum number of plots per page.
#' @param tabular_output If true a table with the information will be the
#' output.
#'
#' @return Two plots per sample: Peptide length distribution and the number of
#'  missed enzymatic cleavages.
#' @export
#'
#' @examples
#' MQPathCombined <- system.file("extdata/combined/", package = "MQmetrics")
#' MQCombined <- make_MQCombined(MQPathCombined)
#' PlotProteaseSpecificity(MQCombined)
PlotProteaseSpecificity <- function(MQCombined,
                                    palette = "Set2",
                                    plots_per_page = 5,
                                    tabular_output = FALSE) {
    peptides <- MQCombined$peptides.txt

    `Missed cleavages` <- value <- variable <- Length <- freq <-  NULL

    peptides <- peptides %>% select(contains(c(
        "Missed cleavages",
        "Experiment",
        "Length"
    )))

    pep_melt <- melt(peptides,
                    id.vars = c("Missed cleavages", "Length"),
                    measure.vars = colnames(peptides %>%
                                        select(contains(c("Experiment"))
                                            )
                                    )
                    )

    pep_melt1 <- aggregate(value ~ variable + `Missed cleavages`,
                        data = pep_melt,
                        sum)

    if (tabular_output == TRUE) {

        missed_summary <- pep_melt1 %>%
        group_by(variable, `Missed cleavages`) %>%
        summarise(freq = sum(value))

        missed_summary <- pivot_wider(missed_summary,
                                    names_from =  `Missed cleavages`,
                                    values_from = freq)

        missed_summary$variable <- gsub('Experiment', '',
                                        missed_summary$variable)

        colnames(missed_summary)[colnames(
            missed_summary)=='variable'] <- 'Experiment'

        return(missed_summary)
    }

    pep_melt1$variable <- gsub("Experiment", "", pep_melt1$variable)

    # Create plot2 for length peptides
    pep_melt2 <- pep_melt
    pep_melt2$value <- 1
    pep_melt2 <- aggregate(value ~ variable + Length, data = pep_melt, sum)

    pep_melt2$variable <- gsub("Experiment", "", pep_melt2$variable)

    n_samples <- length(peptides) - 2

    n_pages_needed <- ceiling(
        n_samples / plots_per_page
    )

    colourCount <- n_samples

    getPalette <- colorRampPalette(brewer.pal(8, palette))

    myplots <- list()

    for (ii in seq_len(n_pages_needed)) {
        if (n_samples < plots_per_page) {
            nrow <- n_samples
        } else {
            nrow <- plots_per_page
        }

        # create plot1 for missed cleavages
        plot_cleavages <- ggplot(pep_melt1, aes(
            x = `Missed cleavages`,
            y = value,
            fill = variable
        )) +
            geom_bar(
                stat = "identity", color = "black",
                show.legend = FALSE
            ) +
            ggtitle(label = "Missed enzymatic cleavages") +
            facet_wrap_paginate(. ~ variable,
                                ncol = 1,
                                nrow = nrow,
                                page = ii) +
            ylab("Peptide Frequency") +
            theme_bw() +
            xlab(label = "Missed Cleavages") +
            scale_fill_manual(values = getPalette(colourCount))

        plot_length <- ggplot(pep_melt2, aes(
            x = Length,
            y = value,
            fill = variable
        )) +
            geom_bar(
                stat = "identity", color = "black",
                show.legend = FALSE
            ) +
            ggtitle(label = "Peptide Length") +
            xlab(label = "Length") +
            ylab("Peptide Frequency") +
            facet_wrap_paginate(. ~ variable,
                                ncol = 1,
                                nrow = nrow,
                                page = ii) +
            theme_bw() +
            xlab(label = "Peptide length") +
            scale_fill_manual(values = getPalette(colourCount))


        # Plot them together
        c <- plot_grid(plot_length, plot_cleavages)
        # Make a title
        title <- ggdraw() + draw_label("Protease Specificity", size = 15)

        #print(plot_grid(title, c, ncol = 1, rel_heights = c(0.1, 1.5)))

        myplots[[ii]] <- plot_grid(title, c, ncol = 1,
                                rel_heights = c(0.1, 1.5))
    }
    return(myplots)
}