#' @method plot checkSex
#' @export
plot.checkSex <- function(x, ...) {
lrr2ploidy <- function(x) 2 * exp(3 * x/2)
ploidy2lrr <- function(x) 2 * log(x/2)/3
tmp <- x$data
tmp$X <- ploidy2lrr(lrr2ploidy(tmp$X) + (2 - lrr2ploidy(x$par$offsetX)))
tmp$Y <- tmp$Y - x$par$offsetY
## Calculate LRR - Ploidy lines
ploidy <- c(0.001, 1, 2, 3, 4, 5)
lrrploidy <- ploidy2lrr(ploidy)
posMeans <- apply(cbind(lrrploidy[1:5], lrrploidy[2:6]), 1, mean)
## Draw the plot
graphics::plot(tmp, col = x$class, xlim = c(lrrploidy[1], lrrploidy[5]), ylim = c(lrrploidy[1],
lrrploidy[5]), ylab = "trimmed mean chrY LRR", xlab = "trimmed mean chrX LRR",
pch = 20)
graphics::abline(v = lrrploidy[2:5], lty = 2)
graphics::abline(h = lrrploidy[2:5], lty = 2)
graphics::text(x = lrrploidy[2:5], y = lrrploidy[1] + 0.1, labels = c("X", "XX", "XXX",
"XXXX"), srt = 90, pos = 4, offset = 0.7)
graphics::text(x = lrrploidy[1] + 0.1, y = lrrploidy[2:5], labels = c("Y", "YY", "YYY",
"YYYY"), pos = 3, offset = 0.1)
graphics::legend("bottomleft", legend = c("Females", "Males"), pch = 20, col = c(1, 2))
}
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