colorBySpecies: Assign colors by SpeciesID
In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

colorBySpecies

R Documentation

Assign colors by SpeciesID

Description

Assigns unique colors by SpeciesID, for multi-species plotting.

Usage

colorBySpecies(speciesSet, palette = c("cyan", "springgreen", "gold", "hotpink"), 
	intergenic = NULL, intergenic.color = "brown")

Arguments

`speciesSet`	a vector of SpeciesIDs, or similar identifiers to factor on
`palette`	a vector of colors to choose from, at least as long as the levels of `speciesSet`
`intergenic`	an optional boolean condition, of the same length as `speciesSet`, that flags which IDs will be colored as 'intergenic'
`intergenic.color`	the color for 'intergenic'

Details

a utility for coloring features of multi-species images, like chromosome or gene pie and bar charts. Lets the speciesID of each feature be color coded without explicitly naming them.

Value

a LIST, with

`colors`	a vector of colors of the same length as `speciesSet`
`legend.colors`	a named vector of the unique colors and their SpeciesIDs, for use in figure legends