Nothing
#' RLE plot
#' @noRd
makeRLEplot <- function(E, log2.data=TRUE, groups=NULL, col.group=NULL,
showTitle=FALSE, title="Relative log expression (RLE) plot",...){
# log2 the data
if (log2.data==TRUE){
message("log2'ing the data")
E <- log2(E)
}
# handle the colours
if (is.null(groups)) mycol <- NULL
else {
if (length(levels(groups)) > length(col.group)) {
warning("More groups than colours: will plot plain")
mycol <- NULL
} else mycol <- col.group[groups]
}
# calculate the median of log2 counts for each gene
g.medians <- apply(E, 1, FUN = median, na.rm = TRUE)
# substract the median of each gene
E.new <- sweep(E, MARGIN=1, STATS=g.medians, FUN='-')
# generate boxplots for all individuals
boxplot(E.new, xaxt="n", las=2, col= mycol, ...)
xtick <- seq(1, ncol(E.new), by=1)
axis(side=1, at=xtick, tick=FALSE, labels=FALSE)
text(x=xtick, par("usr")[3], labels = colnames(data),
srt=90, pos=1, xpd = TRUE, col = mycol, ...)
if (showTitle) mtext(text=title, side=3, line=0.1)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.