getDiscretePaletteObj: Generate a Discrete Color Palette for Seurat Clusters

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Generate a Discrete Color Palette for Seurat Clusters

Description

Generates a discrete color palette for visualizing clusters in a Seurat object, using a specified identity column to determine the number of unique clusters.

Usage

getDiscretePaletteObj(
  ident.used,
  obj,
  palette.used = c("alphabet", "alphabet2", "glasbey", "polychrome", "stepped")[2],
  show.colors = FALSE,
  seed = 1989
)

Arguments

ident.used	Identity column in the Seurat object to base the color palette on.
obj	Seurat object containing clustering information.
palette.used	The palette name to use for color generation. Options include "alphabet", "alphabet2", "glasbey", "polychrome", and "stepped". Default: "alphabet2".
show.colors	If TRUE, displays the generated colors. Default: FALSE.
seed	Seed for random color generation, ensuring reproducibility. Default: 1989.

Value

A character vector of color values corresponding to the number of clusters.

Examples

## Not run: 
if (interactive()) {
  ident.used <- "resolution_1"
  obj <- YourSeuratObject
  colors <- getDiscretePaletteObj(ident.used = ident.used, obj = obj)
  print(colors)
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.