plot.kataegisList: Create a kataegis "rainfall" plot.
In jjellis/GenomicVis: Genomic Visualisation Routines

Description Usage Arguments Details Value Author(s) Examples

Create a kataegis "rainfall" plot.

1 2	plot.kataegisList(x, chr = NA, start = NA, end = NA, all = FALSE, alpha = 0.5, legend = TRUE, colours = kataegis.colours, ...)

`x`	a `kataegisList` object, usually created with the `kataegis` function.
`chr`	Optionally, only process this chromosome
`start`	Optionally, only process from this start point (must be specify together with `chr` and `end`).
`end`	Optionally, only process until this point (must be specify together with `chr` and `start`).
`all`	Plot all types of SNVs, default only C>X and T>X are plotted.
`alpha`	adjust the alpha level of the points
`legend`	If TRUE display a figure legend
`colours`	a function specifying the colours to use in the plot, see the default value (`kataegis.colours`) for an example.
`...`	passed to `plot` function

In its simplest form (plot(x)), this function produces a rainfall plot on the current graphical device. By default, the whole genome is displayed. This can be changed by providing either the chr parameter (to show a specific chromosome) or the chr, start and end parameters to show a specific region of a chromosome (note that all three parameters must be provided).

invisibly return data.frame of SNVs plotted.

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

## Not run: 
vcf.file <- system.file('extdata', 'example.vcf', package = 'GenomicVis')
x <- kategis(vcf.file)
main <- sprintf("Kataegis: %d", length(x$kataegis))
plot(x, main = main)

## End(Not run)