Mercurial > repos > bcclaywell > argo_navis

annotate bin/plot_pact_tree.R @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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1 #!/usr/bin/env Rscript
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2
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3 library(ggplot2)
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4 library(argparse)
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5
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6 parser <- ArgumentParser()
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7 parser$add_argument('-b', '--brewer', help="Specify a color brewer pallete")
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8 parser$add_argument('-c', '--color-spec', help="Specify a deme -> color CSV mapping")
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9 parser$add_argument('-d', '--demes', help="For help with making colors consistent, always know what all the demes are")
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10 parser$add_argument('common')
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11 parser$add_argument('input')
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12 parser$add_argument('output')
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13 args <- parser$parse_args()
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15 # Load shared library
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16 source(args$common)
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17
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18 data <- read.csv(args$input, stringsAsFactors=F)
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19
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20 # Factorify the demes and assign colors
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21 deme.factor <- factorify.deme(data, args=args)
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22 data <- deme.factor$data
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23 deme.colors <- deme.factor$colors
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24
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25 # We will be doing a separate geom data setting for the tip coloring and such
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26 tips.data <- subset(data, klass == "tip")
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27
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28 # Computing some values for getting spacing/padding right for tips
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29 x.range <- abs(min(data$x) - max(data$x))
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30 x.end <- max(data$x) + (x.range * 0.13)
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31 print(c(min(data$x), max(data$x), x.range, x.end))
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32
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33 # Move the tips names over just a touch from the dots
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34 label.nudge <- x.range * 0.01
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36
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37 # Go to town plotting
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38 gg <- ggplot(data, aes(x=x, y=y, color=label, fill=label))
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39 gg <- gg + geom_segment(aes(xend=parent_x, yend=parent_y))
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40 gg <- gg + scale_color_manual(values=deme.colors)
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41 gg <- gg + geom_text(aes(x=x+label.nudge, y=y, label=sequence, hjust=0), color="black", size=1.8)
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42 gg <- gg + geom_point(aes(color=label), data=tips.data)
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43 gg <- gg + theme_bw()
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44 # Add some padding for the label names on right
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45 gg <- gg + xlim(min(data$x), x.end)
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46 gg <- gg + theme(axis.text.y=element_blank(),
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47 axis.ticks.y=element_blank(),
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48 axis.title.y=element_blank(),
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49 legend.position="none")
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50 gg <- gg + xlab("time (units same as tip dates)")
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51 gg <- gg + labs(title="Maximum likelihood ancestral reconstruction")
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52
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53 # Dynamically compute dimensions
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54 n <- dim(tips.data)[1]
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55 print(n)
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56 height <- 9*(n/292) + 3
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58 ggsave(args$output, gg, width=7, height=height)
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