Mercurial > repos > bebatut > plot_barplot

comparison plot_barplot.R @ 0:a8e03ffaaedc draft

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 74beefba9d138c892208b103b52e706ab4313a4a-dirty
author bebatut
date Mon, 18 Apr 2016 10:35:54 -0400
parents
children 7e3103db022d
comparison
equal deleted inserted replaced
-1:000000000000 0:a8e03ffaaedc
1 library('getopt')
2
3 option_specification = matrix(c(
4 'input_file', 'i', 2, 'character',
5 'output_pdf_file', 'p', 2, 'character',
6 'output_png_file', 'o', 2, 'character',
7 'output_svg_file', 's', 2, 'character',
8 'data_column', 'd', 2, 'integer',
9 'names_column', 'n', 2, 'integer',
10 'xlab', 'x', 2, 'character',
11 'col', 'c', 2, 'character',
12 'bottom_margin', 'b', 2, 'integer',
13 'left_margin', 'l', 2, 'integer',
14 'top_margin', 't', 2, 'integer',
15 'right_margin', 'r', 2, 'integer',
16 'header','y',2,'logical'
17 ), byrow=TRUE, ncol=4);
18
19 options = getopt(option_specification);
20
21 header = TRUE
22 if(!is.null(options$header)) header = options$header
23
24 data = read.table(options$input_file, sep = '\t', h = header)
25
26 data_column = 2
27 if(!is.null(options$data_column)) data_column = options$data_column
28 names_column = 1
29 if(!is.null(options$names_column)) names_column = options$names_column
30
31 margin = c(5,19,1,1)
32 if(!is.null(options$bottom_margin)) margin[1] = options$bottom_margin
33 if(!is.null(options$left_margin)) margin[2] = options$left_margin
34 if(!is.null(options$top_margin)) margin[3] = options$top_margin
35 if(!is.null(options$right_margin)) margin[4] = options$right_margin
36
37 xlab = ""
38 if(!is.null(options$xlab)) xlab = options$xlab
39
40 col = "grey"
41 if(!is.null(options$col)) col = options$col
42
43 plot_barplot <- function(){
44 par(las=2)
45 par(mar=margin)
46 barplot(data[, data_column], horiz = T, xlab = xlab,
47 names.arg = data[, names_column], col = col, cex.names=0.7,
48 cex.axis = 0.8)
49 }
50
51 if(!is.null(options$output_pdf_file)){
52 pdf(options$output_pdf_file)
53 plot_barplot()
54 dev.off()
55 }
56
57 if(!is.null(options$output_svg_file)){
58 svg(options$output_svg_file)
59 plot_barplot()
60 dev.off()
61 }