Mercurial > repos > artbio > sr_bowtie_dataset_annotation

comparison barplot.r @ 3:008de522b3ea draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
author artbio
date Sun, 10 Feb 2019 18:31:51 -0500
parents
children e11f91575af6
comparison
equal deleted inserted replaced
2:243ed53cbc0d 3:008de522b3ea
1 if (length(commandArgs(TRUE)) == 0) {
2 system("Rscript barplot.r -h", intern = F)
3 q("no")
4 }
5
6
7 # load packages that are provided in the conda env
8 options( show.error.messages=F,
9 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
10 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
11 warnings()
12 library(optparse)
13 library(ggplot2)
14 library(scales)
15
16
17
18 #Arguments
19 option_list = list(
20 make_option(
21 c("-i", "--input"),
22 default = NA,
23 type = 'character',
24 help = "Input file that contains count data (no header)"
25 ),
26 make_option(
27 c("-o", "--barplot"),
28 default = NA,
29 type = 'character',
30 help = "PDF output file"
31 )
32 )
33
34 opt = parse_args(OptionParser(option_list = option_list),
35 args = commandArgs(trailingOnly = TRUE))
36
37
38 ##
39 annotations = read.delim(opt$input, header=F)
40 colnames(annotations) = c("class", "counts")
41 annotations = cbind(annotations, fraction=annotations$counts/annotations$counts[1])
42 annotations = annotations[-1,]
43 # ggplot2 plotting
44 ggplot(annotations, aes(x="classes", y=fraction, fill=class)) +
45 geom_bar(width = .7, position=position_stack(), stat = "identity") +
46 geom_text(aes(label = percent(fraction)), position = position_stack(vjust = 0.5),size = 4)
47 ggtitle('Class proportions')
48 ggsave(file=opt$barplot, device="pdf")