|
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
|
|
|
7 # 1 2 3 4 5 6 7 8 9 10 11
|
|
|
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
|
|
|
18 #open lib
|
|
|
19 library(Vennerable)
|
|
|
20
|
|
|
21 # for labels of bars or bar groups presume column names from data
|
|
|
22 if (xData != "default") {
|
|
|
23 # read without header input file (must be tabular)
|
|
|
24 annot_data <- read.table(in.file, header=F, sep="\t")
|
|
|
25 colnames (annot_data) <- strsplit(xData,",")[[1]]
|
|
|
26 Vannot <- Venn(annot_data)
|
|
|
27 } else {
|
|
|
28 # read without header input file (must be tabular)
|
|
|
29 annot_data <- read.table(in.file, header=T, sep="\t")
|
|
|
30 Vannot <- Venn(annot_data)
|
|
|
31 }
|
|
|
32
|
|
|
33 #png(out.file,width = 1600, height = 1600, res = resolution)
|
|
|
34 png(out.file, res = resolution)
|
|
|
35
|
|
|
36 # plot it
|
|
|
37 if (plottype == "ChowRuskey") {
|
|
|
38 plot(Vannot, type = plottype)
|
|
|
39
|
|
|
40 } else if (plottype == "AWFE") {
|
|
|
41 plot(Vannot, doWeights = weighting, type = plottype)
|
|
|
42
|
|
|
43 } else if (plottype == "circles") {
|
|
|
44 plot(Vannot)
|
|
|
45
|
|
|
46 } else if (plottype == "ellipses"){
|
|
|
47 plot(Vannot, type = "ellipses")
|
|
|
48
|
|
|
49 } else if (plottype == "squares"){
|
|
|
50 plot(Vannot, type = "squares")
|
|
|
51
|
|
|
52 }
|
|
|
53
|
|
|
54 cat ("version 1.0, info: alex.bossers@wur.nl\n")
|
|
|
55 dev.off()
|
|
|
56
|
