plotKataegis: Plot a kataegis rainfall figure.

Description Usage Arguments Value Author(s) Examples

Description

Create a rainfall plot showing potential regions of kataegis. The input GRanges instance should only contain SNV (i.e., no INDELs) that have a single ALT allele. The input GRanges instance must also contain a valid Seqinfo class that gives the lengths of the chromosomes. The easiest way to obtain this from a VCF file is via the read.vcf function from this package.

Usage

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plotKataegis(x, chr = NULL, all = FALSE, alpha.f = 1,
  colour.map = kataegis.colours, main = NULL, newpage = TRUE,
  panel_colour = "grey90", point_size = unit(4, "point"))

Arguments

x

A GRanges instance containing SNVs.

chr

Create a rainfall plot for a single chromosome specified by this parameter.

all

all

alpha.f

number in (0, 1] specifiying the alpha level with which to draw the points.

colour.map

A list specifying the colours to use in the figure. See kataegis.colours for exact format.

main

Title for plot

newpage

logical. If TRUE create figure on a new device, otherwise print to current device.

panel_colour

Colour of background panels indicating chromosomes.

point_size

specify the size of individual points.

Value

None

Author(s)

Jonathan Ellis <jonathan.j.ellis@gmail.com>

Examples

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library(VariantAnnotation)
vcf.file <- system.file('extdata', 'example.vcf', package = 'GenomicVis')
vcf <- read.vcf(vcf.file, 'GRCh37')
x <- rowData(vcf)
plotKataegis(x)

jjellis/GenomicVis documentation built on May 19, 2019, 11:39 a.m.