Mercurial > repos > miller-lab > genome_diversity

annotate coverage_plot.r @ 32:03c22b722882

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remove BeautifulSoup dependency
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:54:23 -0400
parents 8997f2ca8c7a
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1 args <- commandArgs(TRUE);
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2 output_file <- args[1];
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4 x <- read.table('coverage2.txt', skip=1, sep='\t');
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6 individuals <- dim(x)[1];
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7 max_cov <- dim(x)[2] - 2;
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8 max_val <- max(x[-1]) / 100;
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9 colors <- rainbow(individuals);
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11 line_width = 3;
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12 xt = t(x);
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14 xvals <- c(0:max_cov);
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15 values <- as.numeric(as.vector(xt[,1][-1]))/100;
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17 pdf(file=output_file, onefile=TRUE, width=10, height=6);
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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");
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21 if (individuals > 1) {
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22 for (i in 2:individuals) {
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23 values <- as.numeric(as.vector(xt[,i][-1]))/100;
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24 lines(xvals, values, col=colors[i], lwd=line_width);
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25 }
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26 }
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29 names <- as.vector(t(x[1]));
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30 legend(x='topright', legend=names, fill=colors, bty='n');
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32 dev.off();