diff bin/plot_migration_rates.R @ 0:d67268158946 draft

planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/plot_migration_rates.R	Mon Oct 12 17:43:33 2015 -0400
@@ -0,0 +1,60 @@
+#!/usr/bin/env Rscript
+
+library(argparse)
+library(ggplot2)
+library(gtable)
+
+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$add_argument('stats')
+parser$add_argument('output')
+args <- parser$parse_args()
+
+# Load shared library
+source(args$common)
+
+
+stats <- read.delim(args$stats,
+                    stringsAsFactors=F,
+                    colClasses=c(mean='numeric', lower='numeric', upper='numeric'))
+
+
+# Filter out just the paired migration statistics
+stats <- stats[grepl("mig", stats$statistic),]
+stats <- subset(stats, statistic != "mig_all")
+
+
+# Now let's split this up a bit into mig_from and mig_to
+mig.split <- strsplit(stats$statistic, "_")
+stats$mig_from <- as.character(lapply(mig.split, function(x) x[2]))
+stats$mig_to <- as.character(lapply(mig.split, function(x) x[3]))
+
+deme.factor <- factorify.deme(stats, label='mig_from', args=args)
+stats <- deme.factor$data
+deme.colors <- deme.factor$colors
+
+
+# Now for let there be plots
+gg <- ggplot(stats)
+gg <- gg + geom_crossbar(aes(x=mig_to, y=mean, ymin=lower, ymax=upper, fill=mig_from))
+gg <- gg + facet_grid(mig_from ~ .)
+gg <- gg + scale_fill_manual(values=deme.colors, name="source deme")
+#gg <- gg + scale_y_sqrt()
+gg <- gg + labs(y="")
+gg <- gg + theme_bw()
+gg <- gg + xlab("target deme")
+gg <- gg + labs(title="Migration rate comparison")
+
+
+# Render and save output; with the right hand facet labels on the left instead...
+g <- ggplotGrob(gg)
+g$layout[g$layout$name == "strip-right",c("l", "r")] <- 2
+svg(args$output, width=5, height=4.3)
+  grid.newpage()
+  grid.draw(g)
+dev.off()
+
+