Mercurial > repos > bcclaywell > argo_navis

annotate bin/plot_migration_rates.R @ 2:7eaf6f9abd28 draft default tip

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b-dirty
author bcclaywell
date Mon, 12 Oct 2015 17:57:38 -0400
parents d67268158946
children
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1 #!/usr/bin/env Rscript
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2
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3 library(argparse)
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4 library(ggplot2)
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5 library(gtable)
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6
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7 parser <- ArgumentParser()
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8 parser$add_argument('-b', '--brewer', help="Specify a color brewer pallete")
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9 parser$add_argument('-c', '--color-spec', help="Specify a deme -> color CSV mapping")
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10 parser$add_argument('-d', '--demes', help="For help with making colors consistent, always know what all the demes are")
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11 parser$add_argument('common')
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12 parser$add_argument('stats')
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13 parser$add_argument('output')
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14 args <- parser$parse_args()
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15
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16 # Load shared library
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17 source(args$common)
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20 stats <- read.delim(args$stats,
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21 stringsAsFactors=F,
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22 colClasses=c(mean='numeric', lower='numeric', upper='numeric'))
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25 # Filter out just the paired migration statistics
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26 stats <- stats[grepl("mig", stats$statistic),]
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27 stats <- subset(stats, statistic != "mig_all")
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30 # Now let's split this up a bit into mig_from and mig_to
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31 mig.split <- strsplit(stats$statistic, "_")
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32 stats$mig_from <- as.character(lapply(mig.split, function(x) x[2]))
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33 stats$mig_to <- as.character(lapply(mig.split, function(x) x[3]))
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34
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35 deme.factor <- factorify.deme(stats, label='mig_from', args=args)
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36 stats <- deme.factor$data
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37 deme.colors <- deme.factor$colors
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40 # Now for let there be plots
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41 gg <- ggplot(stats)
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42 gg <- gg + geom_crossbar(aes(x=mig_to, y=mean, ymin=lower, ymax=upper, fill=mig_from))
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43 gg <- gg + facet_grid(mig_from ~ .)
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44 gg <- gg + scale_fill_manual(values=deme.colors, name="source deme")
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45 #gg <- gg + scale_y_sqrt()
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46 gg <- gg + labs(y="")
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47 gg <- gg + theme_bw()
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48 gg <- gg + xlab("target deme")
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49 gg <- gg + labs(title="Migration rate comparison")
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52 # Render and save output; with the right hand facet labels on the left instead...
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53 g <- ggplotGrob(gg)
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54 g$layout[g$layout$name == "strip-right",c("l", "r")] <- 2
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55 svg(args$output, width=5, height=4.3)
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56 grid.newpage()
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57 grid.draw(g)
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58 dev.off()
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