constitutional guides for X/Y chromosomes

[drtconway]

Thanks for making/improving a useful tool.

We found the guides on the whole genome plots confusing for chrX and chrY. I think the following change results in a plot that is easier to interpret. You may wish to incorporate it:

$ git diff
diff --git a/wisecondorX/include/plotter.R b/wisecondorX/include/plotter.R
index f4ac798..45d5059 100644
--- a/wisecondorX/include/plotter.R
+++ b/wisecondorX/include/plotter.R
@@ -130,9 +130,13 @@ plot(1, main="", axes=F, # plots nothing -- enables segments function
      cex=0, ylim=c(chr.wide.lower.limit,chr.wide.upper.limit))
 
 plot.constitutionals <- function(ploidy, start, end){
-  segments(start, log2(1/ploidy), end, log2(1/ploidy), col=color.B, lwd=2, lty=3)
-  segments(start, log2(2/ploidy), end, log2(2/ploidy), col=color.A, lwd=2, lty=3)
-  segments(start, log2(3/ploidy), end, log2(3/ploidy), col=color.C, lwd=2, lty=3)
+  pm1 <- ploidy - 1
+  pp1 <- ploidy + 1
+  if (pm1 > 0) {
+    segments(start, log2(pm1/ploidy), end, log2(pm1/ploidy), col=color.B, lwd=2, lty=3)
+  }
+  segments(start, log2(ploidy/ploidy), end, log2(ploidy/ploidy), col=color.A, lwd=2, lty=3)
+  segments(start, log2(pp1/ploidy), end, log2(pp1/ploidy), col=color.C, lwd=2, lty=3)
 }
 
 genome.len <- chr.ends[length(chr.ends)]
@@ -203,7 +207,7 @@ par(xpd=F)
 par(xpd=NA)
 legend(x=chr.ends[length(chr.ends)] * 0.3,
        y=chr.wide.upper.limit + (abs(chr.wide.upper.limit) + abs(chr.wide.lower.limit)) * 0.23,
-       legend=c("Constitutional 3n", "Constitutional 2n", "Constitutional 1n"),
+       legend=c("Constitutional n+1", "Constitutional n", "Constitutional n-1"),
        text.col=color.X, cex=1.3, bty="n", lty=c(3,3,3), lwd=1.5, col=color.X)
 legend(x=0,
        y=chr.wide.upper.limit + (abs(chr.wide.upper.limit) + abs(chr.wide.lower.limit)) * 0.23,