(BITS-VIB) venn-tools

Standalone R scripts to plot Venn diagrams for 2, 3 or 4 groups from pre-computed counts.

Introduction

These scripts are meant for vizalization of summary counts obtained from CLI applications (e.g. intersect counts between several 'algorithm-X' runs of variant lists obtained by different callers or datasets).

Unlike other such tools, the scripts take the counts passed by command-line arguments to plot the numbers in the corresponding Venn areas. The arguments allow some level of customization like generating white, grey, or colored backgrounds venn diagrams (run with -h for more details).

Requirements

In order to use these scripts, you will need [R] and RScript installed on your computer (done by most package installers including yum and apt-get).

You will also need the following three [R] packages:

gridBase http://cran.r-project.org/web/packages/gridBase/ required for colorfulVennPlot plotting.
colorfulVennPlot http://cran.r-project.org/web/packages/colorfulVennPlot/ to actually plot the Venn diagrams.
optparse http://cran.r-project.org/web/packages/optparse/ to handle command line arguments.

Installing the dependencies is documented on the top of the code. Please read the respective package documentations if you wish to improve these scripts.

How to Use the scripts

Type the script name followed by -h or --help will list all available parameters

2DVenn.R -h

Usage: /opt/biotools/bin/2DVenn.R [options]


Options:
	-a A.COUNT, --a.count=A.COUNT
		counts for A-only

	-b B.COUNT, --b.count=B.COUNT
		counts for B-only

	-i AB.COUNT, --ab.count=AB.COUNT
		counts for AB-intersect

	-A A.LABEL, --a.label=A.LABEL
		label for A

	-B B.LABEL, --b.label=B.LABEL
		label for B

	-t TITLE, --title=TITLE
		Graph Title

	-x FORMAT, --format=FORMAT
		file format for output 1:PNG, 2:PDF [default: 1]

	-o FILE, --file=FILE
		file name for output [default: 2Dvenn.png]

	-u FILL, --fill=FILL
		fill with 1:colors, 2:greys or 3:white [default: 3]

	-h, --help
		Show this help message and exit