PeakPlot {Signac}

Plot peaks in a genomic region

Description

Display the genomic ranges in a ChromatinAssay object that fall in a given genomic region

Usage

PeakPlot(
  object,
  region,
  assay = NULL,
  peaks = NULL,
  group.by = NULL,
  color = "dimgrey",
  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.

peaks

A GRanges object containing peak coordinates. If NULL, use coordinates stored in the Seurat object.

group.by

Name of variable in feature metadata (if using ranges in the Seurat object) or genomic ranges metadata (if using supplied ranges) to color ranges by. If NULL, do not color by any metadata variable.

color

Color to use. If group.by is not NULL, this can be a custom color scale (see examples).

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

# plot peaks in assay
PeakPlot(atac_small, region = "chr1-710000-715000")

# manually set color
PeakPlot(atac_small, region = "chr1-710000-715000", color = "red")

# color by a variable in the feature metadata
PeakPlot(atac_small, region = "chr1-710000-715000", group.by = "count")