heatmapGeneAccessibility: Heatmap Gene Accessibility

View source: R/heatmapGeneAccessibility.R

heatmapGeneAccessibilityR Documentation

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 June 29, 2022, 4:13 p.m.