plotKataegis: Plot a kataegis rainfall figure.
In jjellis/GenomicVis: Genomic Visualisation Routines

Description Usage Arguments Value Author(s) Examples

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.

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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"))

`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.

None

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

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