plot_heatmap_scExp: Plot cell correlation heatmap with annotations

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Plot cell correlation heatmap with annotations

Description

Plot cell correlation heatmap with annotations

Usage

plot_heatmap_scExp(
  scExp,
  name_hc = "hc_cor",
  corColors = (grDevices::colorRampPalette(c("royalblue", "white", "indianred1")))(256),
  color_by = NULL,
  downsample = 1000,
  hc_linkage = "ward.D"
)

Arguments

scExp	A SingleCellExperiment Object
name_hc	Name of the hclust contained in the SingleCellExperiment object
corColors	A palette of colors for the heatmap
color_by	Which features to add as additional bands on top of plot
downsample	Number of cells to downsample
hc_linkage	A linkage method for hierarchical clustering. See cor. ('ward.D')

Value

A heatmap of cell to cell correlation, grouping cells by hierarchical clustering.

Examples

data("scExp")
plot_heatmap_scExp(scExp)

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.