AnnotationPlot: Plot gene annotations

In Signac: Analysis of Single-Cell Chromatin Data

Plot gene annotations

Description

Display gene annotations in a given region of the genome.

Usage

AnnotationPlot(
  object,
  region,
  assay = NULL,
  mode = "gene",
  sep = c("-", "-"),
  extend.upstream = 0,
  extend.downstream = 0
)

Arguments

object	A Seurat object
region	A genomic region to plot
assay	Name of assay to use. If NULL, use the default assay.
mode	Display mode. Choose either "gene" or "transcript" to determine whether genes or transcripts are plotted.
sep	Separators to use for strings encoding genomic coordinates. First element is used to separate the chromosome from the coordinates, second element is used to separate the start from end coordinate.
extend.upstream	Number of bases to extend the region upstream.
extend.downstream	Number of bases to extend the region downstream.

Value

Returns a ggplot object

Examples

AnnotationPlot(object = atac_small, region = c("chr1-29554-39554"))

Signac documentation built on Sept. 11, 2024, 9:30 p.m.