R/CS_bin_plot.R

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

#' Plot CS bin counts
#' 
#' Plot Credible Set bins counts for multiple fine-mapping method results.
#' @param merged_DT Merged fine-mapping results data from
#'  \link[echolocatoR]{finemap_loci}.
#' @param show_plot Show plot. 
#'
#' @family summarise
#' @export 
#' @importFrom stats setNames
#' @importFrom methods show
#' @importFrom echodata get_CS_bins
#' @examples
#' dat <- echodata::BST1 
#' dat$Locus <- "BST1"
#' bin_plot <- echoannot::CS_bin_plot(merged_DT = dat)
CS_bin_plot <- function(merged_DT,
                        show_plot = TRUE) {
    
    requireNamespace("ggplot2")
    Method <- bin <- ..count.. <- NULL;
    
    bin_counts <- echodata::get_CS_bins(merged_DT = merged_DT)
    # Assign bin colors 
    used_bins <- levels(bin_counts$bin)[levels(bin_counts$bin) %in%
        unique(bin_counts$bin)]
    custom_colors <- palette_gnbu(n = length(levels(bin_counts$bin)))
    custom_colors_dict <- stats::setNames(
        custom_colors[seq(1, length(used_bins))],
        rev(used_bins)
    )
    custom_colors_dict[names(custom_colors_dict) == "0"] <- "lightgray"

    bin_plot <- ggplot2::ggplot(
        subset(bin_counts, Method != "mean"),
        ggplot2::aes(x = Method, fill = bin)
    ) +
        ggplot2::geom_bar(
            stat = "count", show.legend = TRUE,
            position = ggplot2::position_stack(reverse = FALSE), color = "white"
        ) +
        # scale_fill_brewer(palette = "Spectral", direction = -1) +
        ggplot2::scale_fill_manual(values = custom_colors_dict) +
        # geom_text(aes(label = paste(bin,"SNPs")),
        # position =  position_stack(vjust = .5), vjust=-1, stat = "count") +
        ggplot2::geom_text(ggplot2::aes(label = ..count..),
            position = ggplot2::position_stack(vjust = .5),
            vjust = .5, stat = "count"
        ) +
        ggplot2::theme_bw() +
        ggplot2::labs(x = NULL, y = "Loci", fill = "CS size") +
        ggplot2::coord_flip() +
        ggplot2::theme(
            panel.grid.major = ggplot2::element_blank(),
            panel.grid.minor = ggplot2::element_blank(),
            rect = ggplot2::element_blank(),
            axis.text.x = ggplot2::element_blank(),
            axis.ticks = ggplot2::element_blank(),
            legend.position = "top"
        ) +
        ggplot2::guides(fill = ggplot2::guide_legend(nrow = 1, reverse = TRUE))
    if (show_plot) suppressWarnings(methods::show(bin_plot))
    return(list(
        plot = bin_plot,
        data = bin_counts
    ))
}