R/track_scaffold_window_snp_ratio.R

Defines functions track_scaffold_window_snp_ratio

Documented in track_scaffold_window_snp_ratio

#' @title Scaffold ratio SNP window track
#'
#' @description Draws a scaffold plot track for the ratio of SNP window data.
#' This function is intended for use in the \code{\link{draw_scaffold_plot}} function.
#'
#' @param data SNP window data frame.
#'
#' @param scaffold.name Name of the plotted scaffold (for the x axis)
#'
#' @param region A vector specifying the boundaries of the region to be plotted, e.g. c(125000, 250000).
#'
#' @param major.lines.y If TRUE, major grid lines will be plotted for the y axis (default: TRUE).
#'
#' @param major.lines.x If TRUE, major grid lines will be plotted for the y axis (default: TRUE).
#'
#' @param ylim Limits of the y axis (default: c(min(FST), 1)).
#'
#' @param males.color Color of the plotted area for males (default: "dodgerblue3").
#'
#' @param females.color Color of the plotted area for females (default: "firebrick2").
#'
#' @param bottom.track If TRUE, this track will be considered bottom track of the plot and the x axis will be drawn (default: FALSE).


track_scaffold_window_snp_ratio <- function(data,
                                            scaffold.name,
                                            region,
                                            major.lines.y = TRUE,
                                            major.lines.x = FALSE,
                                            ylim = NULL,
                                            males.color = "dodgerblue3",
                                            females.color = "firebrick2",
                                            bottom.track = FALSE) {

    # Create major grid lines for y axis if specified
    if (major.lines.y) {
        major_lines_y <- ggplot2::element_line(color = "grey90", linetype = 1)
    } else {
        major_lines_y <- ggplot2::element_blank()
    }

    # Create major grid lines for x axis if specified
    if (major.lines.x) {
        major_lines_x <- ggplot2::element_line(color = "grey90", linetype = 1)
    } else {
        major_lines_x <- ggplot2::element_blank()
    }

    # Separate male and female biased ratio for color
    # Formula for SNP ratio. The base SNP ratio is given a weight based on the absolute difference between Males and Females SNPs
    data$Ratio <- log((1 + data$Males) / (1 + data$Females), 2) * log(1 + abs(data$Males - data$Females), 2) ^ 2
    data$Ratio_m <- data$Ratio
    data$Ratio_m[which(data$Ratio_m < 0)] <- 0
    data$Ratio_f <- data$Ratio
    data$Ratio_f[which(data$Ratio_f > 0)] <- 0

    # Y axis limits
    ymax <- 1.1 * max(abs(data$Ratio))
    ylim <- c(-ymax, ymax)

    # Add x axis if bottom track
    if (!bottom.track) {
        axis_title_x <- ggplot2::element_blank()
    } else {
        axis_title_x <- ggplot2::element_text()
    }

    # Draw the plot
    g <- ggplot2::ggplot() +
        cowplot::theme_cowplot() +
        ggplot2::geom_ribbon(data = data, ggplot2::aes(x = Original_position, ymin = 0, ymax = Ratio_m),
                             fill = males.color, color = males.color, size = 0.4, alpha = 0.75) +
        ggplot2::geom_ribbon(data = data, ggplot2::aes(x = Original_position, ymin = 0, ymax = Ratio_f),
                             fill = females.color, color = females.color, size = 0.4, alpha = 0.75) +
        ggplot2::scale_y_continuous(name = expression(paste("log"[2], "(M:F) SNPs window")), expand = c(0.01, 0.01), limits = ylim,
                                    breaks = seq(-ymax, ymax, 2 * ymax / 6), labels = round(seq(-ymax, ymax, 2 * ymax / 6))) +
        generate_x_scale(region, scaffold.name) +
        ggplot2::theme(axis.text.y = ggplot2::element_text(margin = ggplot2::margin(l = 5)),
                       panel.grid.major.y = major_lines_y,
                       panel.grid.major.x = major_lines_x,
                       axis.title.x = axis_title_x)

    return(g)
}
INRA-LPGP/PoolSex-vis documentation built on March 7, 2020, 6:03 p.m.