ExprColors: Generate colors for multi-color marker expression labeling in...

In EmbedSOM: Fast Embedding Guided by Self-Organizing Map

Generate colors for multi-color marker expression labeling in a single plot

Description

Generate colors for multi-color marker expression labeling in a single plot

Usage

ExprColors(
  exprs,
  base = exp(1),
  scale = 1,
  cutoff = 0,
  pow = NULL,
  col = ClusterPalette(dim(exprs)[2], alpha = alpha),
  nocolor = grDevices::rgb(0.75, 0.75, 0.75, alpha/2),
  alpha = 0.5
)

Arguments

exprs	Matrix-like object with marker expressions (extract it manually from your data)
base, scale	Base(s) and scale(s) for softmax (convertible to numeric vectors of size 1+ncol(exprs))
cutoff	Gray level (expressed in sigmas of the sample distribution)
pow	Obsolete, now renamed to scale.
col	Colors to use, defaults to colors taken from 'ClusterPalette'
nocolor	The color to use for sub-gray-level expression, default gray.
alpha	Default alpha value.

Examples

d <- cbind(rnorm(1e5), rexp(1e5))
EmbedSOM::PlotEmbed(d, col=EmbedSOM::ExprColors(d, pow=2))

EmbedSOM documentation built on July 5, 2022, 5:14 p.m.