R/plot_snpasso_and_genes2.R

In duytpm16/qtl2utils: Modification of QTL2 Plots

# two-panel plot with both snp asso and genes
# (for a single chromosome)
#
# calls plot_snpasso and plot_genes
# internal function that is called by plot_snpasso
plot_snpasso_and_genes2 <-
  function(scan1output, snpinfo, max_peak, haplo_peak_drop = NULL, haplo_scan = NULL, show_all_snps=TRUE,
           drop_hilit=NA, col_hilit="violetred", col="darkslateblue",
           gap=25, minlod=0, text_cex = .2,
           genes, minrow=4, padding=0.2,
           colors=c("black", "red3", "green4", "blue3", "darkorange2"),
           scale_pos=1, start_field="start", stop_field="stop",
           strand_field="strand", name_field="Name",
           top_panel_prop=0.65, xlim=NULL, xaxt="s",
           xlab=NULL, main="", sub="", ...)
  {
    # 2 x 1 panels; adjust margins
    old_mfrow <- par("mfrow")
    old_mar <- par("mar")
    on.exit(par(mfrow=old_mfrow, mar=old_mar))
    layout(rbind(1,2), heights=c(top_panel_prop, 1-top_panel_prop))
    top_mar <- bottom_mar <- old_mar
    top_mar[1] <- 0.1
    bottom_mar[3] <- 0.1

    if(is.null(xlim)) xlim <- range(snpinfo$pos)

    if(is.null(xlab)) {
      if(length(unique(snpinfo$chr))==1)
        xlab <- paste("Chr", snpinfo$chr[1], "position (Mbp)")
      else
        xlab <- "Position (Mbp)"
    }


    par(mar=top_mar)
    plot_snpasso2(scan1output, snpinfo, max_peak = max_peak, haplo_peak_drop = haplo_peak_drop,
                  show_all_snps=show_all_snps, drop_hilit=drop_hilit, col_hilit=col_hilit, col=col,
                  gap=gap, minlod=minlod, xlim=xlim, ylim=c(0,range(scan1output)[2]+2),
                  xaxt="n", xlab="", text_cex = text_cex,  main=main, ...)

    if(!is.null(haplo_scan)){
      par(new = T)
      plot(haplo_scan$pos, haplo_scan[,1], type = 'l', xlim = xlim, axes = FALSE, ann=FALSE)
      axis(side = 4)
    }

    par(mar=bottom_mar)

    plot_genes2(genes, snp_lod = scan1output, haplo_peak_drop = haplo_peak_drop, max_peak = max_peak, scan1output = scan1output, snpinfo = snpinfo,
                minrow=minrow, padding=padding, colors=colors, scale_pos=scale_pos, start_field=start_field,
                stop_field=stop_field, strand_field=strand_field, name_field=name_field, xlim=xlim,
                xaxt=xaxt, xlab=xlab, sub=sub, text_cex = text_cex, ...)

  }