Mercurial > repos > bcclaywell > argo_navis

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b-dirty
author bcclaywell
date Mon, 12 Oct 2015 17:57:38 -0400
parents d67268158946
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
1 #!/usr/bin/env Rscript
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
2
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
3 library(argparse)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
4 library(ggplot2)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
5
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
6 parser <- ArgumentParser()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
7 parser$add_argument('-b', '--brewer', help="Specify a color brewer pallete")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
8 parser$add_argument('-c', '--color-spec', help="Specify a deme -> color CSV mapping")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
9 parser$add_argument('-d', '--demes', help="For help with making colors consistent, always know what all the demes are")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
10 parser$add_argument('common')
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
11 parser$add_argument('input', help="Skyline outputs")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
12 parser$add_argument('stats', help="Contains tmrca mean, which we use for cutting stats")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
13 parser$add_argument('output')
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
14 args <- parser$parse_args()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
15
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
16 # Load shared library
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
17 source(args$common)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
18
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
19
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
20 data <- read.csv(args$input, stringsAsFactors=F, sep="\t")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
21 stats.data <- read.csv(args$stats, stringsAsFactors=F, sep="\t")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
22
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
23 tmrca.mean <- subset(stats.data, statistic == "tmrca")$mean
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
24
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
25 data <- subset(data, time > -tmrca.mean)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
26 data$statistic <- gsub("pro_(.*)", "\\1", data$statistic)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
27
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
28 deme.factor <- factorify.deme(data, label='statistic', args=args)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
29 data <- deme.factor$data
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
30 deme.colors <- deme.factor$colors
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
31
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
32 gg <- ggplot(data, aes(x=time, y=mean, fill=statistic))
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
33 gg <- gg + geom_bar(stat="identity")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
34 gg <- gg + scale_fill_manual(values=deme.colors, name="deme")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
35 gg <- gg + theme_bw()
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
36 gg <- gg + xlab("evolutionary distance")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
37 gg <- gg + ylab("ancestral deme proportion")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
38 gg <- gg + labs(title="Skyline proportions histogram")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
39
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
40 ggsave(args$output, gg, width=7, height=4.3)
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
41