diff bin/plot_skyline_hist.R @ 0:d67268158946 draft

planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/plot_skyline_hist.R	Mon Oct 12 17:43:33 2015 -0400
@@ -0,0 +1,41 @@
+#!/usr/bin/env Rscript
+
+library(argparse)
+library(ggplot2)
+
+parser <- ArgumentParser()
+parser$add_argument('-b', '--brewer', help="Specify a color brewer pallete")
+parser$add_argument('-c', '--color-spec', help="Specify a deme -> color CSV mapping")
+parser$add_argument('-d', '--demes', help="For help with making colors consistent, always know what all the demes are")
+parser$add_argument('common')
+parser$add_argument('input', help="Skyline outputs")
+parser$add_argument('stats', help="Contains tmrca mean, which we use for cutting stats")
+parser$add_argument('output')
+args <- parser$parse_args()
+
+# Load shared library
+source(args$common)
+
+
+data <- read.csv(args$input, stringsAsFactors=F, sep="\t")
+stats.data <- read.csv(args$stats, stringsAsFactors=F, sep="\t")
+
+tmrca.mean <- subset(stats.data, statistic == "tmrca")$mean
+
+data <- subset(data, time > -tmrca.mean)
+data$statistic <- gsub("pro_(.*)", "\\1", data$statistic)
+
+deme.factor <- factorify.deme(data, label='statistic', args=args)
+data <- deme.factor$data
+deme.colors <- deme.factor$colors
+
+gg <- ggplot(data, aes(x=time, y=mean, fill=statistic))
+gg <- gg + geom_bar(stat="identity")
+gg <- gg + scale_fill_manual(values=deme.colors, name="deme")
+gg <- gg + theme_bw()
+gg <- gg + xlab("evolutionary distance")
+gg <- gg + ylab("ancestral deme proportion")
+gg <- gg + labs(title="Skyline proportions histogram")
+
+ggsave(args$output, gg, width=7, height=4.3)
+