scatterEnrichment: Generate a density-based scatter plot

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

Generate a density-based scatter plot

Description

This function allows to the user to examine the distribution of 2 gene sets along the x.axis and y.axis. The color gradient is generated using the a density estimate. See ggpointdensity) for more information.

Usage

scatterEnrichment(
  input.data,
  assay = NULL,
  x.axis = NULL,
  y.axis = NULL,
  scale = FALSE,
  facet.by = NULL,
  style = "point",
  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.
x.axis	Gene set to plot on the x.axis.
y.axis	Gene set to plot on the y.axis. group.by parameter or use the gene.set name if wanting to apply a gradient palette.
scale	Visualize raw values FALSE or Z-transform enrichment values TRUE.
facet.by	Variable to facet the plot into n distinct graphs.
style	Return a "hex" bin plot or a "point"-based plot.
palette	Colors to use in visualization - input any hcl.pals.

Value

ggplot2 object with a scatter plot of selected gene.sets

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)
                        
scatterEnrichment(pbmc_small, 
                  assay = "escape",
                  x.axis = "Tcells",
                  y.axis = "Bcells")

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