Plot GEP usage in reduced dimension space

Plot GEP usage in reduced dimension space

Usage

plotGEPUsage(x, name = "cNMF", k = NULL, programs = 1:4, reduction = "UMAP")

Arguments

x

A SingleCellExperiment object with cNMF results

name

Character, name of the cNMF result (default "cNMF")

k

Integer, which k value to use. If NULL, uses optimal k

programs

Integer vector, which programs to plot (default 1:4)

reduction

Character, which reducedDim to use for coordinates (default "UMAP")

Value

ggplot2 object

Examples

# sce <- runConsensusNMF(sce, k_range = 5:10)
# sce <- runUMAP(sce)
# plotGEPUsage(sce, programs = 1:4, reduction = "UMAP")