getClusterColours: Get a vector of cluster colours, optionally highlighting...
In fungenomics/cytobox: A toolbox for analyzing single cell RNA-seq data

Description Usage Arguments Value Author(s) Examples

Given a seurat object, get a named character vector of cluster colours, where names are cluster names (coresponding to levels(seurat@ident)), and values are hex codes of the colours, either the default colours from Seurat, or colours you specify. This is trivial to make this yourself, so this is used as a utility function for retaining the colours of clusters you want to highlight, and setting the colours of all other clusters to grey, or another default, non-intrusive colour.

1 2	getClusterColours(seurat, clusters = NULL, original_colours = NULL, default_colour = "gray80")

`seurat`	Seurat object
`clusters`	Vector of one or more clusters to highlight, matching the levels at `levels(seurat@ident)`. If "none", returns `default_colour` for every clusters. Default: all clusters, obtained from `levels(seurat@ident)`.
`original_colours`	(Optional) Vector of colours to use. Either one colour per cluster, in the order of `levels(seurat@ident)`, or one colour per cluster passed to `clusters`, in the other they were provided. Default: default ggplot2 colours used by Seurat.
`default_colour`	Colour to use for non-highlighted clusters Default: gray80 (light grey).

Named character vector

Selin Jessa

# Trivial: get named character vector with default colours
getClusterColours(pbmc)

# Highlight clusters 2 and 3
getClusterColours(pbmc, clusters = c(2, 3))

# Highlight clusters 2 and 3, set all other cluster colours to white
getClusterColours(pbmc, clusters = c(2, 3), default_colour = "white")