|
0
|
1 #!/usr/bin/R
|
|
|
2
|
|
|
3 # R script to call Vennerable package from galaxy
|
|
|
4 # info: alex.bossers@wur.nl
|
|
|
5
|
|
|
6 # R --slave --vanilla --file=PlotBar.R --args inputFile x_data weighting outputFile plottype resolution imagetype
|
|
|
7 # 1 2 3 4 5 6 7 8 9 10 11 12
|
|
|
8
|
|
|
9 #get cmd line args
|
|
|
10 args <- commandArgs()
|
|
|
11 in.file <- args[6]
|
|
|
12 xData <- args[7] # data labels xData of format "a, b, c" and can include spaces
|
|
|
13 weighting <- args[8]
|
|
|
14 out.file <- args[9]
|
|
|
15 plottype <- args[10]
|
|
|
16 resolution <- args[11] # in dpi
|
|
|
17 imagetype <- args[12] # svg, pdf or png
|
|
|
18
|
|
|
19 #open lib
|
|
|
20 library(Vennerable)
|
|
|
21 options(bitmapType='cairo')
|
|
|
22
|
|
|
23 # for labels of bars or bar groups presume column names from data
|
|
|
24 if (xData != "default") {
|
|
|
25 # read without header input file (must be tabular)
|
|
|
26 annot_data <- read.table(in.file, header=F, sep="\t")
|
|
|
27 colnames (annot_data) <- strsplit(xData,",")[[1]]
|
|
|
28 Vannot <- Venn(annot_data)
|
|
|
29 } else {
|
|
|
30 # read without header input file (must be tabular)
|
|
|
31 annot_data <- read.table(in.file, header=T, sep="\t")
|
|
|
32 Vannot <- Venn(annot_data)
|
|
|
33 }
|
|
|
34
|
|
|
35 #set output imagetype (svg pdf or png)
|
|
|
36 #R 3.0.2 and default cairo libs should handle it all ok
|
|
|
37 #it could be that X11 should be loaded for non-pdf
|
|
|
38 if (imagetype == "svg") {
|
|
|
39 svg(out.file)
|
|
|
40 } else if (imagetype == "png") {
|
|
|
41 png(out.file, width = 1600, height = 1600, res = resolution)
|
|
|
42 } else {
|
|
|
43 pdf(out.file)
|
|
|
44 }
|
|
|
45
|
|
|
46 # plot it
|
|
|
47 if (plottype == "ChowRuskey") {
|
|
|
48 plot(Vannot, type = plottype)
|
|
|
49
|
|
|
50 } else if (plottype == "AWFE") {
|
|
|
51 plot(Vannot, doWeights = weighting, type = plottype)
|
|
|
52
|
|
|
53 } else if (plottype == "circles") {
|
|
|
54 plot(Vannot)
|
|
|
55
|
|
|
56 } else if (plottype == "ellipses"){
|
|
|
57 plot(Vannot, type = "ellipses")
|
|
|
58
|
|
|
59 } else if (plottype == "squares"){
|
|
|
60 plot(Vannot, type = "squares")
|
|
|
61
|
|
|
62 } else if (plottype == "battle"){
|
|
|
63 plot(Vannot, type = "battle")
|
|
|
64 }
|
|
|
65
|
|
|
66 cat ("Wrapper version 1.2, running Vennerable v3.0-82\n Info/bugs: alex.bossers@wur.nl\n")
|
|
|
67 dev.off()
|
