Plot peaks in a genomic region — PeakPlot • Signac

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

Usage

PeakPlot(
  object,
  region,
  assay = NULL,
  peaks = NULL,
  group.by = NULL,
  color = "dimgrey",
  extend.upstream = 0,
  extend.downstream = 0
)

Arguments

object: A SeuratObject::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).
extend.upstream: Number of bases to extend the region upstream.
extend.downstream: Number of bases to extend the region downstream.

Value

Returns a ggplot2::ggplot() object

Examples

# \donttest{
# 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")

# }