do_EnrichmentHeatmap() | Gene set enrichment heatmaps

Enrichment heatmaps display averaged enrichment scores for gene sets across groups. This function computes enrichment scores using Seurat’s AddModuleScore (or UCell) and aggregates them by metadata variables.

Basic usage

gene_lists <- list(
  "IPC.like"      = c("CDC25C", "KIF18B", "KIF14", "CENPE"),
  "Cilia.like" = c("DNAAF1", "ADGB", "CFAP61", "CFAP157"),
  "OPC.like" = c("KCNQ5", "MEOX2", "MBP", "SNTG1"),
  "Mesenchymal.like" = c("S100A1", "MGP", "TNNT1", "H2AFJ")
)

p <- SCpubr::do_EnrichmentHeatmap(sample = sample,
                                  input_gene_list = gene_lists,
                                  flip = TRUE)
p

Multiple grouping variables

p <- SCpubr::do_EnrichmentHeatmap(sample = sample,
                                  input_gene_list = gene_lists,
                                  group.by = c("Annotation", "subtype"),
                                  flip = TRUE)
p

Scoring methods

Use flavor = "Seurat" or flavor = "UCell" to toggle different scoring methods.

Scale scores

Transform scores to 0-1 range for easier comparison:

p <- SCpubr::do_EnrichmentHeatmap(sample = sample,
                                  input_gene_list = gene_lists,
                                  scale_scores = TRUE, 
                                  flip = TRUE)
p

Display values

p <- SCpubr::do_EnrichmentHeatmap(sample = sample,
                                  input_gene_list = gene_lists,
                                  values.show = TRUE,
                                  values.threshold = 0.5,
                                  flip = TRUE)
p

Return enriched object

Get the Seurat object with computed enrichment scores:

result <- SCpubr::do_EnrichmentHeatmap(sample = sample,
                                       input_gene_list = gene_lists,
                                       return_object = TRUE)

p <- result$plot
sample_enriched <- result$object

Parameter reference

Note

For parameters shared across many functions (color palettes, typography, legend styling), see Shared features.

Core parameters

Parameter Description Default
input_gene_list Named list of gene signatures —

Scoring method

Parameter Description Default
flavor Scoring method ("Seurat" or "UCell") "Seurat"
nbin Number of bins (Seurat) 24
ctrl Control genes per bin (Seurat) 100
ncores CPU cores for UCell 1
storeRanks Store ranks for faster UCell TRUE
scale_scores Scale scores to 0-1 range FALSE

Clustering & ordering

Parameter Description Default
cluster Hierarchically cluster TRUE
features.order Custom gene set order NULL
groups.order Custom group order NULL

Output

Parameter Description Default
return_object Return Seurat object with scores FALSE

See also