plotMetaPrograms: Visualizations for meta-programs

In GeneNMF: Non-Negative Matrix Factorization for Single-Cell Omics

Visualizations for meta-programs

Description

Generates a clustered heatmap for meta-program similarities (by Jaccard index or Cosine similarity). This function is intended to be run on the object generated by getMetaPrograms, which contains a pre-calculated tree of pairwise similarities between clusters (as a 'hclust' object).

Usage

plotMetaPrograms(
  mp.res,
  similarity.cutoff = c(0, 1),
  scale = "none",
  downsample = 1000,
  showtree = TRUE,
  palette = viridis(100, option = "A", direction = -1),
  annotation_colors = NULL,
  main = "Clustered Heatmap",
  show_rownames = FALSE,
  show_colnames = FALSE,
  ...
)

Arguments

mp.res	The meta-programs object generated by getMetaPrograms
similarity.cutoff	Min and max values for similarity metric
scale	Heatmap rescaling (passed to pheatmap as 'scale')
downsample	Limit max number of samples in heatmap, to avoid overloading the graphics
showtree	Whether to plot the hierarchical clustering tree
palette	Heatmap color palette (passed to pheatmap as 'color')
annotation_colors	Color palette for MP annotations
main	Heatmap title
show_rownames	Whether to display individual program names as rows
show_colnames	Whether to display individual program names as cols
...	Additional parameters for pheatmap

Value

Returns a clustered heatmap of MP similarities, in ggplot2 format

Examples

library(Seurat)
data(sampleObj)
geneNMF_programs <- multiNMF(list(sampleObj), k=5)
geneNMF_metaprograms <- getMetaPrograms(geneNMF_programs, nMP=3)
plotMetaPrograms(geneNMF_metaprograms)

GeneNMF documentation built on April 4, 2025, 4:39 a.m.