# contrastPlot_bk = function(hub,
# chrfilter=NULL,
# bplower=NULL,
# bpupper=NULL,
# bonferroni=FALSE,
# threshold=0.001,
# lowerPbonfer = FALSE,
# forceRecalc = TRUE
# ) {
#
# dat = cleanByChrPvalsBonfer(
# hub = hub,
# threshold = threshold,
# sameChr = sameChr,
# lowerPbonfer = lowerPbonfer,
# forceRecalc = forceRecalc,
# bpdiff = bpdiff
# )
#
# # Take single-SNP data from hub, and QCDH data from dat
# filter0 = rep(TRUE, nrow(hub$chr))
# filter = rep(TRUE, nrow(dat))
# if(! is.null(chrfilter)) {
# filter0 = hub$chr[, 1] %in% chrfilter
# filter = dat$chr %in% chrfilter
# }
# if(! is.null(bplower)) {
# filter0 = filter0 & hub$bp[, 1] >= bplower
# filter = filter & dat$bp >= bplower
# }
# if(! is.null(bpupper)) {
# filter0 = filter0 & hub$bp[, 1] <= bpupper
# filter = filter & dat$bp <= bpupper
# }
# if(! is.null(threshold)) {
# filter0 = filter0 & hub$pvals[, 1] <= threshold
# filter = filter & dat$p <= threshold
# }
#
# filter0 = which(filter0)
# filter = which(filter)
#
# chrvec0 = hub$chr[filter0, 1]
# chrvec = dat$chr[filter]
# bpvec0 = hub$bp[filter0, 1]
# bpvec = dat$bp[filter]
#
# colorvec = c(rep("Single SNP", length(filter0)), rep("QCDH", length(filter)))
#
# basepvalsvec = hub$pvals[filter0, 1]
# if(bonferroni) {
# minpvalvec = dat$pbonfer[filter]
# } else {
# minpvalvec = dat$p[filter]
# }
#
# chrvec = c(chrvec0, chrvec)
# bpvec = c(bpvec0, bpvec)
# pvalsvec = c(basepvalsvec, minpvalvec)
#
# posorder = order(chrvec, bpvec)
# chrvec = chrvec[posorder]
# bpvec = bpvec[posorder]
# pvalsvec = pvalsvec[posorder]
# colorvec = colorvec[posorder]
#
# resinfo = mqinfo(chr=chrvec, bp=bpvec, p=pvalsvec, colorvec=colorvec)
# hub$contrastPlotOut = suppressWarnings(mh(resinfo))
# hub$contrastPlotOut
# }
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