heatmapEnrichment: Generate a heatmap to visualize enrichment values

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

Generate a heatmap to visualize enrichment values

Description

This function allows to the user to examine the heatmap with the mean enrichment values by group. The heatmap will have the gene sets as rows and columns will be the grouping variable.

Usage

heatmapEnrichment(
  input.data,
  assay = NULL,
  group.by = NULL,
  gene.set.use = "all",
  cluster.rows = FALSE,
  cluster.columns = FALSE,
  facet.by = NULL,
  scale = FALSE,
  summary.stat = "mean",
  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.
group.by	Categorical parameter to plot along the x.axis. If input is a single-cell object the default will be cluster.
gene.set.use	Selected gene sets to visualize. If "all", the heatmap will be generated across all gene sets.
cluster.rows	Use Euclidean distance to order the row values.
cluster.columns	Use Euclidean distance to order the column values.
facet.by	Variable to facet the plot into n distinct graphs.
scale	Visualize raw values FALSE or Z-transform enrichment values TRUE.
summary.stat	Use 'median' or 'mean' values to display.
palette	Colors to use in visualization - input any hcl.pals.

Value

ggplot2 object with heatmap of mean enrichment values

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)
                        
heatmapEnrichment(pbmc_small, 
                  assay = "escape")

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