view vennerable/unused/Vennerable.R_backup_png_xml @ 0:77bbf955e8de default tip

initial commit

#!/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
# 1     2       3             4           5       6        7       8         9        10        11

#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
	
#open lib
library(Vennerable)

# 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)
}

#png(out.file,width = 1600, height = 1600, res = resolution)
png(out.file, res = resolution)

# 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")

}

cat ("version 1.0, info: [e-mail]\n")
dev.off()