splitEnrichment: Visualize enrichment results with a split violin plot

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

Visualize enrichment results with a split violin plot

Description

This function allows to the user to examine the distribution of enrichment across groups by generating a split violin plot.

Usage

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

Arguments

input.data	Enrichment output from escape.matrix or runEscape.
assay	Name of the assay to plot if data is a single-cell object.
split.by	Variable to form the split violin, must have 2 levels.
group.by	Categorical parameter to plot along the x.axis. If input is a single-cell object the default will be cluster.
gene.set	Gene set to plot (on y-axis).
order.by	Method to organize the x-axis - "mean" will arrange the x-axis by the mean of the gene.set, while "group" will arrange the x-axis by in alphanumerical order. Using NULL will not reorder the x-axis.
facet.by	Variable to facet the plot into n distinct graphs.
scale	Visualize raw values FALSE or Z-transform enrichment values TRUE.
palette	Colors to use in visualization - input any hcl.pals.

Value

ggplot2 object violin-based distributions of selected gene.set

Examples

GS <- list(Bcells = c("MS4A1", "CD79B", "CD79A", "IGH1", "IGH2"),
           Tcells = c("CD3E", "CD3D", "CD3G", "CD7","CD8A"))
pbmc_small <- SeuratObject::pbmc_small
pbmc_small <- runEscape(pbmc_small, 
                        gene.sets = GS, 
                        min.size = NULL)
                        
splitEnrichment(pbmc_small, 
                assay = "escape",
                split.by = "groups",
                gene.set = "Tcells")

ncborcherding/escape documentation built on Dec. 1, 2024, 8:12 a.m.