R/krsa_reverse_krsa_plot.R

In CogDisResLab/KRSA: KRSA: Kinome Random Sampling Analyzer

#' Generates the reverse krsa plot (to examine kinase activity)
#'
#' This function takes in chipCov df, the LFC table, kinases, LFC threshold, and generates the reverse krsa plot (to examine kinase activity)
#'
#' @param chipCov chipCov df for eaither STK or PTK
#' @param lfc_table the LFC table
#' @param kinases vector of kinases
#' @param lfc_thr LFC threshold
#' @param byChip will facet by Barcode
#' @param facet facet by chip
#'
#' @return ggplot object
#'
#' @family plots
#'
#' @export
#'
#' @examples
#' TRUE
krsa_reverse_krsa_plot <- function(chipCov, lfc_table, kinases, lfc_thr, byChip = T, facet = F) {
    if (byChip == T) {
        lfc_table$colMean <- cut(lfc_table$totalMeanLFC, breaks = c(-Inf, -1 * lfc_thr, lfc_thr, Inf), labels = c("red", "black", "red"))
        lfc_table$colFC <- cut(lfc_table$LFC, breaks = c(-Inf, -1 * lfc_thr, lfc_thr, Inf), labels = c("black", "gray", "black"))
    } else {
        lfc_table$colFC <- cut(lfc_table$LFC, breaks = c(-Inf, -1 * lfc_thr, lfc_thr, Inf), labels = c("red", "black", "red"))
    }

    chipCov %>%
        dplyr::filter(Kin %in% kinases) %>%
        dplyr::rename(Peptide = "Substrates") -> KinHitPeps

    dplyr::left_join(KinHitPeps, lfc_table, by = "Peptide") -> combined_data

    if (byChip == T && facet == T) {
        combined_data %>%
            dplyr::filter(!is.na(totalMeanLFC)) %>%
            dplyr::select(Kin, Peptide, totalMeanLFC, colMean, Barcode) %>%
            dplyr::rename(LFC = totalMeanLFC, colFC = colMean) %>%
            dplyr::distinct() -> combined_data
    } else if (byChip == T && facet == F) {
        combined_data %>%
            dplyr::filter(!is.na(totalMeanLFC)) %>%
            dplyr::select(Kin, Peptide, totalMeanLFC, colMean) %>%
            dplyr::rename(LFC = totalMeanLFC, colFC = colMean) %>%
            dplyr::distinct() -> combined_data
    } else {
        combined_data %>%
            dplyr::select(Kin, Peptide, LFC, colFC) %>%
            dplyr::distinct() -> combined_data
    }


    combined_data %>%
        ggplot2::ggplot(ggplot2::aes(Kin, LFC)) +
        ggplot2::geom_jitter(ggplot2::aes(color = colFC), position = ggplot2::position_jitter(width = .1), show.legend = F) +
        ggplot2::geom_hline(yintercept = lfc_thr, linetype = "dashed") +
        ggplot2::geom_hline(yintercept = -1 * lfc_thr, linetype = "dashed") +
        ggplot2::labs(
            y = "Log2 Fold Change",
            x = ""
        ) +
        ggplot2::theme(
            axis.text.x = ggplot2::element_text(size = 4, angle = 30)
        ) +
        ggplot2::scale_colour_identity() +
        ggplot2::theme_bw() -> gg

    if (byChip == T && facet == T) {
        gg + ggplot2::facet_wrap(~Barcode)
    } else {
        gg
    }
}