GeneNMF (version 0.8.0)

plotMetaPrograms: 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,
  ...
)

Value

Returns a clustered heatmap of MP similarities, in ggplot2 format

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

Examples

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