splitEnrichment: Plot Enrichment Distributions Using Split or Dodged Violin...

In ncborcherding/escape: Easy single cell analysis platform for enrichment

Plot Enrichment Distributions Using Split or Dodged Violin Plots

Description

Visualize the distribution of gene set enrichment scores across groups using violin plots. When 'split.by' contains exactly two levels, the function draws split violins for easy group comparison within each 'group.by' category. If 'split.by' has more than two levels, standard dodged violins are drawn instead.

Usage

splitEnrichment(
  input.data,
  assay = NULL,
  split.by = NULL,
  group.by = NULL,
  gene.set.use = NULL,
  order.by = NULL,
  facet.by = NULL,
  scale = TRUE,
  palette = "inferno"
)

Arguments

input.data	Output of escape.matrix or a single‑cell object previously processed by runEscape.
assay	Name of the assay holding enrichment scores when 'input.data' is a single‑cell object. Ignored otherwise.
split.by	A metadata column used to split or color violins. Must contain at least two levels. If it contains more than two, dodged violins are used.
group.by	Metadata column plotted on the *x*‑axis. Defaults to the Seurat/SCE 'ident' slot when 'NULL'.
gene.set.use	Character(1). Name of the gene set to display.
order.by	How to arrange the x‑axis: *'"mean"'* – groups ordered by decreasing group mean; *'"group"'* – natural sort of group labels; *'NULL'* – keep original ordering.
facet.by	Optional metadata column used to facet the plot.
scale	Logical; if 'TRUE' scores are centred/scaled (Z‑score) prior to plotting.
palette	Character. Any palette from hcl.pals.

Value

A [ggplot2] object.

Examples

gs <- list(Bcells = c("MS4A1", "CD79B", "CD79A", "IGH1", "IGH2"),
           Tcells = c("CD3E", "CD3D", "CD3G", "CD7","CD8A"))
           
pbmc <- SeuratObject::pbmc_small |>
  runEscape(gene.sets = gs, min.size = NULL)

splitEnrichment(input.data = pbmc,
                assay = "escape",
                split.by = "groups",
                gene.set.use = "Tcells")

ncborcherding/escape documentation built on June 12, 2025, 1 p.m.