--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coverage_plot.r	Fri Sep 28 11:57:18 2012 -0400
@@ -0,0 +1,31 @@
+x <- read.table('coverage2.txt', skip=1, sep='\t')
+
+individuals <- dim(x)[1]
+max_cov <- dim(x)[2] - 2
+max_val <- max(x[-1]) / 100
+colors <- rainbow(individuals)
+
+line_width = 3
+xt = t(x)
+
+xvals <- c(0:max_cov)
+values <- as.numeric(as.vector(xt[,1][-1]))/100
+
+pdf(file='coverage.pdf', onefile=TRUE, width=10, height=6);
+
+plot(xvals, values, type='l', ylim=c(0, max_val), xlim=c(0, max_cov), col=colors[1], lwd=line_width, xlab="Coverage", ylab="Proportion")
+
+if (individuals > 1) {
+    for (i in 2:individuals) {
+        values <- as.numeric(as.vector(xt[,i][-1]))/100;
+        lines(xvals, values, col=colors[i], lwd=line_width);
+    }
+}
+
+
+names <- as.vector(t(x[1]))
+legend(x='topright', legend=names, fill=colors, bty='n')
+
+dev.off()
+
+