bedr (version 1.0.2)

bedr.plot.region: Visualize regions or intervals

Description

Visualize regions or intervals. e.g. VennDiagrams of intersections of distinct intervals, base pairs and genes.

Usage

bedr.plot.region(
	input,
	filename = NULL,
	type = "venn",
	feature = "interval",
	fraction.overlap = 0.000000001,
	group = NULL,
	params = list(),
	verbose = TRUE
	)

Arguments

input

A list of input regions or indices

filename

The name of the output image file

type

The type of plot. only 'venn' is supported for intersections at the moment.

feature

How should the regions be intersected. By unique "interval", "gene", "size" or "other" to use the features in the first item in the input list.

fraction.overlap

Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).

group

A grouping parameter for barplots. Possible values include "input", "chr", or a categorical vector of length equal to the sum of the input.

params

Additional parameters for plotting or intersecting. See venn.diagram function for possible options.

verbose

Include text messages.

Value

Plots!

Details

By default a venn diagram is output. If a single input is used then the plot shows the number of unique and collapsed regions after applying a merge.

Examples

if (check.binary("bedtools")) {
	# example data
	a <- get.random.regions(n = 1000, chr = "chr22", size.mean = 10)
	b <- get.random.regions(n = 1000, chr = "chr22", size.mean = 10)
	d <- get.random.regions(n = 1000, chr = "chr22", size.mean = 10)
	e <- get.random.regions(n = 1000, chr = "chr22", size.mean = 10)
	f <- get.random.regions(n = 1000, chr = "chr22", size.mean = 10)

	pdf("bedr.plot.region.ex.pdf")

	# basic venn diagrams
	bedr.plot.region(input = list(a=a,b=b))
	bedr.plot.region(input = list(a=a,b=b,d=d))
	#bedr.plot.region(input = list(a=a,b=b,d=d,e=e))
	#bedr.plot.region(input = list(a=a,b=b,d=d,e=e,f=f))

	### change venn parameters
	bedr.plot.region(
		input = list(a=a,b=b,d=d),
		params = list(lty = 2, label.col = "black", main = "Region Overlap")
		)

	### try with different 
	#bedr.plot.region(input = list(a=a,b=b), feature = "gene")
	#bedr.plot.region(input = list(a=a,b=b), feature = "reference")
	#bedr.plot.region(input = list(a=a,b=b), feature = "interval")
	#bedr.plot.region(input = list(a=a,b=b), feature = "cluster")
	#bedr.plot.region(input = list(a=a,b=b), feature = "bp")

	dev.off()
	}