getVariantsColors: getVariantsColors

In bernatgel/karyoploteR: Plot customizable linear genomes displaying arbitrary data

getVariantsColors

Description

Given the reference and alternative for a set of variants, assigns a color to each of them

Usage

getVariantsColors(ref, alt, color.table=NULL, color.schema=c("cell21breast"))

Arguments

ref	(character vector) The reference nucleotides of the variants. It has to have the same length as alt.
alt	(character vector) The alternative nucleotides of the variants. It has to have the same length as ref
color.table	(named character vector) if present, its used to assign colors to the nucleotide substitutions.
color.schema	(character) The name of the color schema to use: cell21breast (the color schema used in "Mutational Processes Molding the Genomes of 21 Breast Cancers" by S. Nik-Zainal, Cell, 2012). (defaults to cell21breast)

Details

The function creates an nucleotide substitution identifier with for each variant and uses it to query the color.table lookup table. If color.table is NULL, a color.table based in the selected color.schema is used. All unkwonwn nucleotide substitutions are assigned a gray color. Color table needs to have entries for C>A, C>G, C>T, T>A, T>C and T>G (and optionally "others"), since other changes can be reverse complemented to these.

Value

a named character vector with the colors associated to each variant

See Also

plotKaryotype, kpPlotRainfall

Examples

 
ref <- c("A", "A", "C", "T", "G", "A")
alt <- c("G", "C", "T", "A", "A", "-")
getVariantsColors(ref, alt)

col.table <- c("C>A"="#FF0000", "C>G"="#000000", "C>T"="#00FF00", "T>A"="#0000FF", "T>C"="#BB00BB", "T>G"="#00BBBB", "other"="#888888")
getVariantsColors(ref, alt, col.table)

bernatgel/karyoploteR documentation built on Feb. 1, 2024, 11:48 p.m.