heatmapGeneAccessibility: Heatmap Gene Accessibility

In FertigLab/ATACCoGAPS: Analysis Tools for scATACseq Data with CoGAPS

Heatmap Gene Accessibility

Description

Use the output from geneAccessibility function to plot a heatmap of the accessible peaks for a particular gene.

Usage

heatmapGeneAccessibility(
  genePeaks,
  celltypes,
  colColors = NULL,
  order = TRUE,
  ...
)

Arguments

genePeaks	The peaks corresponding to a singular gene; one element of the list ouptut by geneAccessibility()
celltypes	List or factor of celltypes corresponding to the cells in the scATAC-seq data set the peaks were found in
colColors	A vector of colors to color the celltypes by, if NULL a random vector of colors is generated
order	should the data be ordered by the celltype classifier? TRUE by default
...	additional arguments to the heatmap.2 function from the gplots package

Value

A plot of the peaks overlapping with a particular gene of interest

Examples

library(Homo.sapiens)
geneList <- c("TAL1", "EGR1")
data(schepGranges)
data("subsetSchepData")
data(schepCellTypes)
accessiblePeaks <- geneAccessibility(geneList = geneList,
 peakGranges = schepGranges, atacData = subsetSchepData, genome = Homo.sapiens)
heatmapGeneAccessibility(genePeaks = accessiblePeaks$EGR1, celltypes = schepCellTypes)

FertigLab/ATACCoGAPS documentation built on Feb. 8, 2023, 6:46 p.m.