do_ActivityHeatmap() | Activity scores heatmap

Activity heatmaps display gene set activity scores computed using decoupleR. Input a named list of gene sets and the function computes activity scores per cell, then aggregates them by group for visualization.

Basic usage

# Define gene sets
gene_sets <- list(
  "IPC.like"      = c("CDC25C", "KIF18B", "KIF14", "CENPE", "POLQ"),
  "Cilia.like" = c("DNAAF1", "ADGB", "CFAP61", "CFAP157", "CFAP46"),
  "OPC.like" = c("KCNQ5", "MEOX2", "MBP", "SNTG1", "KCNIP1"),
  "Mesenchymal.like" = c("S100A1", "MGP", "TNNT1", "H2AFJ", "KCNIP1")
)

p <- SCpubr::do_ActivityHeatmap(sample = sample,
                                input_gene_list = gene_sets)
p

Group by custom variable

p <- SCpubr::do_ActivityHeatmap(sample = sample,
                                input_gene_list = gene_sets,
                                group.by = "subtype")
p

Subsample cells

p <- SCpubr::do_ActivityHeatmap(sample = sample,
                                input_gene_list = gene_sets,
                                subsample = 1000)
p

Show values

p <- SCpubr::do_ActivityHeatmap(sample = sample,
                                input_gene_list = gene_sets,
                                values.show = TRUE,
                                values.threshold = 4)
p

Return data object

result <- SCpubr::do_ActivityHeatmap(sample = sample,
                                     input_gene_list = gene_sets,
                                     return_object = TRUE)

# Access the plot
result$plot

# Access activity data
result$activities

Parameter reference

Note

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

Core parameters

Parameter Description Default
input_gene_list Named list of gene sets —
statistic DecoupleR statistic "ulm"
flavor Scoring method: "Seurat" or "UCell" "Seurat"
return_object Return data along with plot FALSE

Subsampling

Parameter Description Default
subsample Number of cells to sample 2500
nbin Number of bins for scoring 24
ctrl Control genes per bin 100

Values display

Parameter Description Default
values.show Show numeric values FALSE
values.threshold Threshold on which the text changes color NULL
values.round Decimal places 1

See also