R/PlotiRT.R

In BioAlvaro/MQmetrics: Quality Control of Protemics Data

#' Max intensities of the iRT peptides in each sample.
#'
#' @param MQCombined Object list containing all the files from the MaxQuant
#' output. It is the result from using \code{make_MQCombined}.
#' @param show_calibrated_rt If TRUE, it will also show the calibrated retention
#'  time of each iRT peptide. By default = FALSE.
#' @param tolerance Error maximum to find the iRT peptides by m/z value.
#'  by default is 0.001.
#' @param plots_per_page Establish the maximum number of plots per page.
#'
#' @return A plot showing the iRT peptide in each sample vs the Retention time.
#' @export
#'
#' @examples
#' MQPathCombined <- system.file("extdata/combined/", package = "MQmetrics")
#' MQCombined <- make_MQCombined(MQPathCombined)
#' PlotiRT(MQCombined)
PlotiRT <- function(MQCombined,
                    show_calibrated_rt = FALSE,
                    tolerance = 0.001,
                    plots_per_page = 5) {
    evidence <- MQCombined$evidence.txt

    Experiment <- `m/z` <- `Retention time` <- Sequence <- Intensity <- NULL
    `Calibrated retention time` <- value <- variable <- NULL

    iRT.mZ <- c(
        487.2571, 547.2984, 622.8539, 636.8695, 644.8230, 669.8384,
        683.8282, 683.8541, 699.3388, 726.8361, 776.9301
    )

    names(iRT.mZ) <- Sequence <- c(
        "LGGNEQVTR",
        "YILAGVENSK",
        "GTFIIDPGGVIR",
        "GTFIIDPAAVIR",
        "GAGSSEPVTGLDAK",
        "TPVISGGPYEYR",
        "VEATFGVDESNAK",
        "TPVITGAPYEYR",
        "DGLDAASYYAPVR",
        "ADVTPADFSEWSK",
        "LFLQFGAQGSPFLK")

    names_Sequence <- names(Sequence) <- c(
        "iRT Kit_a",
        "iRT Kit_d",
        "iRT Kit_i",
        "iRT Kit_k",
        "iRT Kit_b",
        "iRT Kit_e",
        "iRT Kit_c",
        "iRT Kit_f",
        "iRT Kit_g",
        "iRT Kit_h",
        "iRT Kit_l"
    )

    irt_names_table <- data.frame(Sequence, names_Sequence)
    # Check for the iRT peptides by sequence
    indexes_prot <- which(evidence$Sequence %in% Sequence)

    # if no iRT peptide found return error.
    if (length(indexes_prot) == 0) {
        message("No iRT peptides found in the MaxQuant output.")
        return(NULL)
    } else {

        # obtain rows only with irt by sequence
        iRT_table_prot <- evidence[indexes_prot, ]

        # remove rows with NA in intensity
        iRT_table_prot <- iRT_table_prot[complete.cases(
            iRT_table_prot$Intensity), ]

        # make table smaller
        iRT_table_prot <- iRT_table_prot %>% select(c( Experiment,
                                                    `m/z`,
                                                    `Retention time`,
                                                    `Calibrated retention time`,
                                                    Sequence,
                                                    Intensity))

        # from the irt obtained, filter them by the theoretical m/z with
        # tolerance
        in_range <- unlist(sapply(iRT_table_prot$`m/z`,
                        function(x) x[any(abs(x - iRT.mZ) < tolerance)]))


        # Obtain the indexes and final table
        indexes <- which(iRT_table_prot$`m/z` %in% in_range)


        iRT_table_prot_final <- iRT_table_prot[indexes, ]

        iRT_table_prot_final <- merge(iRT_table_prot_final,
                                    irt_names_table,
                                    by = "Sequence")

        # obtain the maximum intensity values for each experiment, and sequence.
        iRT_table_prot_maxvalues <- iRT_table_prot_final %>%
            group_by(Experiment, Sequence) %>%
            filter(Intensity == max(Intensity))

        ## Paginate
        # samples for paginate

        n_samples <-length(unique(iRT_table_prot_maxvalues$Experiment))

        n_pages_needed <- ceiling(n_samples / plots_per_page)

        myplots <- list()

        for (ii in seq_len(n_pages_needed)) {

            if (n_samples < plots_per_page) {
                nrow <- n_samples
            } else {
                nrow <- plots_per_page
            }

            p <- ggplot(iRT_table_prot_maxvalues, aes(y = Intensity,
                                                    colour = names_Sequence))+
                geom_point(aes(x = `Retention time`), size = 2) +
                geom_segment(aes(x = `Retention time`,
                                xend = `Retention time`,
                                yend = 0)) +
                facet_wrap_paginate(. ~ Experiment, ncol = 1, page = ii,
                                    nrow = nrow) +
                ggtitle("Biognosys iRT peptides in each sample.") +
                theme_bw() +
                labs(colour = "iRT peptides") +
                theme(legend.position = "bottom")

            if (show_calibrated_rt == TRUE) {
                irt_melted <- melt(iRT_table_prot_maxvalues,
                                    id.vars = c("Sequence",
                                                "Experiment",
                                                "m/z",
                                                "names_Sequence",
                                                "Intensity"))
                p <- ggplot(irt_melted, aes(x = value, y = Intensity,
                                        colour = names_Sequence)) +
                        geom_point(aes(shape = variable), size = 2) +
                        geom_segment(aes(x = value, xend = value, yend = 0)) +
                        facet_wrap_paginate(. ~ Experiment, ncol = 1, page = ii,
                                            nrow = nrow) +
                        ggtitle("Biognosys iRT peptides in each sample.") +
                        theme_bw() +
                        labs(colour = "iRT peptides") +
                        theme(legend.position = "bottom")
                }
        myplots[[ii]] <- p
        }
        return(myplots)
    }

}