Mercurial > repos > miller-lab > genome_diversity

comparison coverage_plot.r @ 27:8997f2ca8c7a

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Update to Miller Lab devshed revision bae0d3306d3b
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 15 Jul 2013 10:47:35 -0400
parents 2c498d40ecde
children
comparison
equal deleted inserted replaced
26:91e835060ad2 27:8997f2ca8c7a
1 x <- read.table('coverage2.txt', skip=1, sep='\t') 1 args <- commandArgs(TRUE);
2 output_file <- args[1];
2 3
3 individuals <- dim(x)[1] 4 x <- read.table('coverage2.txt', skip=1, sep='\t');
4 max_cov <- dim(x)[2] - 2
5 max_val <- max(x[-1]) / 100
6 colors <- rainbow(individuals)
7 5
8 line_width = 3 6 individuals <- dim(x)[1];
9 xt = t(x) 7 max_cov <- dim(x)[2] - 2;
8 max_val <- max(x[-1]) / 100;
9 colors <- rainbow(individuals);
10 10
11 xvals <- c(0:max_cov) 11 line_width = 3;
12 values <- as.numeric(as.vector(xt[,1][-1]))/100 12 xt = t(x);
13 13
14 pdf(file='coverage.pdf', onefile=TRUE, width=10, height=6); 14 xvals <- c(0:max_cov);
15 values <- as.numeric(as.vector(xt[,1][-1]))/100;
15 16
16 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") 17 pdf(file=output_file, onefile=TRUE, width=10, height=6);
18
19 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");
17 20
18 if (individuals > 1) { 21 if (individuals > 1) {
19 for (i in 2:individuals) { 22 for (i in 2:individuals) {
20 values <- as.numeric(as.vector(xt[,i][-1]))/100; 23 values <- as.numeric(as.vector(xt[,i][-1]))/100;
21 lines(xvals, values, col=colors[i], lwd=line_width); 24 lines(xvals, values, col=colors[i], lwd=line_width);
22 } 25 }
23 } 26 }
24 27
25 28
26 names <- as.vector(t(x[1])) 29 names <- as.vector(t(x[1]));
27 legend(x='topright', legend=names, fill=colors, bty='n') 30 legend(x='topright', legend=names, fill=colors, bty='n');
28 31
29 dev.off() 32 dev.off();
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