plotChrRegions: Plot chromosomal regions of interest

In htSeqTools: Quality Control, Visualization and Processing for High-Throughput Sequencing data

Description

Produces a plot with all chromosomes for a given organism, marking regions of interest in a user-specified color.

Usage

plotChrRegions(regions, chrLength, markColor='red', ...)

Arguments

regions	RangedData object with chromosome, start and end positions (chromosome must be stored in space(regions).
chrLength	Named integer vector with chromosome lengths in base pairs.
markColor	Color to be used to mark the regions in the chromosome.
...	Further parameters passed on to plot.

Value

This function produces a plot.

Examples

set.seed(1)
chr <- rep(c('chr1','chr2'),each=10)
chrLength <- c(chr1=10000,chr2=5000)
st <- c(runif(10,1,10000),runif(10,1,5000))
regions <- RangedData(IRanges(st,st+50),space=chr)

plotChrRegions(regions,chrLength=chrLength)

htSeqTools documentation built on May 6, 2019, 3:39 a.m.