annotate vennerable/Vennerable.R @ 0:f21d51d28d8d

initial commit on Vennerable on toolshed

#!/usr/bin/R

# R script to call Vennerable package from galaxy
# info: [e-mail]

# R --slave --vanilla --file=PlotBar.R --args inputFile x_data weighting outputFile plottype resolution imagetype
# 1     2       3             4           5       6        7       8         9        10        11         12

#get cmd line args
args <- commandArgs()
	in.file	<- args[6]
	xData		<- args[7]   # data labels xData of format "a, b, c" and can include spaces
	weighting	<- args[8] 
	out.file	<- args[9]
	plottype	<- args[10]
	resolution	<- args[11] # in dpi
	imagetype	<- args[12] # svg, pdf or png

#open lib
library(Vennerable)
options(bitmapType='cairo')

# for labels of bars or bar groups presume column names from data
if (xData != "default") {
	# read without header input file (must be tabular)
	annot_data <- read.table(in.file, header=F, sep="\t")
	colnames (annot_data) <- strsplit(xData,",")[[1]]
	Vannot <- Venn(annot_data)
} else {
	# read without header input file (must be tabular)
	annot_data <- read.table(in.file, header=T, sep="\t")
	Vannot <- Venn(annot_data)
}

#set output imagetype (svg pdf or png)
#R 3.0.2 and default cairo libs should handle it all ok
#it could be that X11 should be loaded for non-pdf
if (imagetype == "svg") {
    svg(out.file)
} else if (imagetype == "png") {
    png(out.file, width = 1600, height = 1600, res = resolution)
} else {
    pdf(out.file)
}

# plot it
if (plottype == "ChowRuskey") {
	plot(Vannot, type = plottype)

} else if (plottype == "AWFE") {
	plot(Vannot, doWeights = weighting, type = plottype)

} else if (plottype == "circles") {
	plot(Vannot)

} else if (plottype == "ellipses"){
	plot(Vannot, type = "ellipses")

} else if (plottype == "squares"){
	plot(Vannot, type = "squares")

} else if (plottype == "battle"){
        plot(Vannot, type = "battle")
}

cat ("Wrapper version 1.2, running Vennerable v3.0-82\n Info/bugs: [e-mail]\n")
dev.off()