Nothing
################################################################################
# Given a set of significance thresholds and chr lengths that have been used
# in a plot, draw the significance lines.
# NOTE: A QTL PLOT MUST HAVE BEEN DRAWN ALREADY.
# Daniel Gatti
# dan.gatti@jax.org
# Oct. 26, 2015
################################################################################
add.sig.thr = function(sig.thr, sig.col = "red", chrsum) {
# If sig.thr is a matrix, then we have separate autosome and X thresholds.
if(is.matrix(sig.thr)) {
# Make sure that the thresholds and colors have the same length.
if(length(sig.col) < nrow(sig.thr)) {
stop(paste("The number of colors is less than the number of thresholds.",
"Please provide as many colors as there are rows in the sig.thr matrix."))
} # if(length(sig.col) < nrow(sig.thr))
# Get the coordinates to the end of the autosomes.
old.warn = options("warn")$warn
options(warn = -1)
tmp = as.numeric(names(chrsum))
auto.len = max(chrsum[!is.na(tmp)])
X.len = max(chrsum[is.na(tmp)])
options(warn = old.warn)
for(i in 1:nrow(sig.thr)) {
lines(x = c(0, auto.len), y = rep(sig.thr[i,"A"], 2), lwd = 2,
col = sig.col[i])
lines(x = c(auto.len, X.len), y = rep(sig.thr[i,"X"], 2), lwd = 2,
col = sig.col[i])
} # for(i)
} else {
# Make sure that the thresholds and colors have the same length.
if(length(sig.col) < length(sig.thr)) {
stop(paste("The number of colors is less than the number of thresholds.",
"Please provide as many colors as there are thresholds in sig.thr."))
} # if(length(sig.col) < nrow(sig.thr))
abline(h = sig.thr, lwd = 2, col = sig.col)
} # else
} # add.sig.thr
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