Plotting QTL.R

xlim = c(0, 10641881)
ylim = c(0, max(sapply(qtl, function(z) { max(z$p.value) })))

plot <- loop.hs.qtl(qtl = qtl, title = "su")


loop.hs.qtl = function(qtl, title, bin.width = 1000, ...) {
        library(GenomicRanges)
        library(BSgenome.Mmusculus.UCSC.mm10)
        new.qtl = NULL
        for(chr in 1:length(qtl)) {

                print(chr)

                # Create SNP bins with given bin.width
                brks = cut(x = 1:length(qtl[[chr]]), breaks = length(qtl[[chr]]) / bin.width)
                # Split up the SNP positions and get the mean.
                pos = split(start(qtl[[chr]]), brks)
                pos = sapply(pos, mean)
                # Split up the p-values and get the max.
                pv = split(mcols(qtl[[chr]])$p.value, brks)
                pv = sapply(pv, min)

                # Make a single new GRanges object to return.
                gr = GRanges(seqnames = seqnames(qtl[[chr]])[1],
                             ranges = IRanges(start = pos, width = 1), p.value = pv)

                if(chr == 1) {
                        new.qtl = gr
                } else {
                        new.qtl = c(new.qtl, gr)
                } # else

        } # for(chr)

        # Get the chromosome lengths.
        chrlen = seqlengths(BSgenome.Mmusculus.UCSC.mm10)
        names(chrlen) = sub("^chr", "", names(chrlen))
        chrlen = chrlen[seqlevels(new.qtl)] * 1e-6

        # Add the chr lengths to the chromosomes for plotting.
        # Switch positions to genome Mb.
        gmb = start(new.qtl) * 1e-6
        for(chr in 2:length(chrlen)) {

                wh = which(seqnames(new.qtl) == names(chrlen)[chr])
                gmb[wh] = gmb[wh] + sum(chrlen[1:(chr - 1)])

        } # for(chr)

        # Get chromosome mid-points for plotting the Chr name.
        chrmid = (chrlen / 2) + cumsum(c(1, chrlen[-length(chrlen)]))

        # Make the plot.
        col = rep(rgb(0,0,0), length(new.qtl))
        even.chr = which(seqnames(new.qtl) %in% (1:10 * 2))
        col[even.chr] = rgb(0.7,0.7,0.7)
        plot(gmb, -log10(new.qtl$p.value), pch = 20, xaxt = "n",
             col = col, las = 1, xlab = "", ylab = "-log10(p-value)", main = "title")
        mtext(side = 1, line = 0.5, at = chrmid, text = names(chrlen), cex = 1.2)

        return(new.qtl)

}