#' Plot of MADloy object
#'
#' This function plots the summarized LRR of a set of samples
#'
#' @param print.labels should sample labels be showed
#' @param threshold threshold to draw sample labels
#' @param cex.label size of the labels
#' @method plot MADloy
#' @export
plot.MADloy <- function(x, labels, print.labels=FALSE,
threshold = -0.6, cex.label=0.8, ...) {
ss <- 1:length(x$mLRRY)
d <- x$mLRRY
if (missing(labels))
labels <- names(d)
ref <- GenomeInfoDb::seqnames(x$par$ref.region)
ref <- ifelse( length(GenomeInfoDb::seqnames(x$par$ref.region)) == 22 , "Autosomes", paste(GenomeInfoDb::seqnames(x$par$ref.region), collapse="_"))
plot.default(ss, d, type = "n", xlab = "Individuals",
ylab = "Trimmed mean normalized mLRR-Y")
points(ss, d, pch = 16)
abline(h=0, lty=2, col="red")
alt <- d <= threshold
alt[is.na(alt)] <- FALSE
if (any(alt) & print.labels) {
if (requireNamespace("wordcloud", quietly = TRUE) & sum(alt)>1) {
wordcloud::textplot(x = ss[alt], y = d[alt],
words = tools::file_path_sans_ext(labels[alt]),
cex = cex.label,
new = FALSE, xlim=c(min(ss), max(ss)),
ylim=c(min(d[alt]), max(d[alt])))
} else {
text(ss[alt], jitter(d[alt]), tools::file_path_sans_ext(labels[alt]),
cex = cex.label, adj = 0)
}
}
}
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