R/krsa_coverage_plot.R

In CogDisResLab/KRSA: KRSA: Kinome Random Sampling Analyzer

#' Generates a coverage plot (Percentage of total coverage of kinases on chip)
#'
#' This function takes in the chipCov map, Z score table, and chip type to produce a coverage plot (Percentage of total coverage of kinases on chip)
#'
#' @param chipCov df of kinase mapping for either STK or PTK chip
#' @param Ztable Z score table
#' @param chipType type of chip, either STK or PTK
#'
#' @return ggplot object
#'
#' @family plots
#'
#' @export
#'
#' @examples
#' TRUE
krsa_coverage_plot <- function(chipCov, Ztable, chipType = c("STK", "PTK")) {
    chipCov %>%
        dplyr::count(Kin, name = "count") %>%
        dplyr::mutate(Perc = (count / ifelse(chipType == "STK", 141, 193)) * 100) %>%
        dplyr::rename(Kinase = Kin) %>%
        dplyr::left_join(dplyr::select(Ztable, -Z, -method), by = "Kinase") %>%
        dplyr::distinct() %>%
        dplyr::mutate(MeanZ = AvgZ) %>%
        dplyr::filter(!Kinase %in% c("VRK2", "BARK1")) %>%
        dplyr::mutate(breaks = cut(abs(MeanZ),
            breaks = c(0, 1, 1.5, 2, Inf), right = F,
            labels = c("Z <= 1", "1 >= Z < 1.5", "1.5 >= Z < 2", "Z >= 2")
        )) %>%
        ggplot2::ggplot(ggplot2::aes(x = stats::reorder(Kinase, count), Perc, fill = breaks)) +
        ggplot2::geom_col() +
        ggplot2::scale_fill_brewer(palette = "Reds", drop = F, guide = ggplot2::guide_legend(reverse = TRUE, title = "")) +
        ggplot2::geom_text(ggplot2::aes(label = paste0("Z = ", round(MeanZ, 2))), hjust = -0.15, size = 2.2) +
        ggplot2::coord_flip() +
        ggplot2::geom_hline(yintercept = 25, linetype = "dashed", alpha = 1 / 5) +
        ggplot2::geom_hline(yintercept = 50, linetype = "dashed", alpha = 1 / 5) +
        ggplot2::geom_hline(yintercept = 75, linetype = "dashed", alpha = 1 / 5) +
        ggplot2::scale_y_continuous(expand = c(0, 0), labels = function(x) paste0(x, "%"), limits = c(0, 102)) +
        ggplot2::labs(
            x = "Kinases",
            y = "Percentage of Chip Coverage"
        ) +
        ggplot2::theme(
            axis.text.y = ggplot2::element_text(size = 7),
            legend.title = ggplot2::element_blank()
        ) +
        ggplot2::theme_bw()
}