bedr.plot.region: Visualize regions or intervals

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

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.

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.

Value

Plots!

Author(s)

Daryl Waggott

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()
	}

Example output

sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied


######################
#### bedr v1.0.3 ####
######################

checking binary availability...
  * Checking path for bedtools... FAIL
  * Checking path for bedops... FAIL
  * Checking path for tabix... FAIL
tests and examples will be skipped on R CMD check if binaries are missing

  * Checking path for bedtools... sh: 1: cannot create /dev/null: Permission denied
FAIL

bedr documentation built on May 2, 2019, 11:36 a.m.