#' @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)
}
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