Generate coverage plot within an interval across different cell types

get_coverage_plot(
  object = NULL,
  region = NULL,
  features = NULL,
  links = FALSE,
  ranges.group.by = "seurat_cluster",
  peaks = FALSE,
  bigwig = NULL,
  region.highlight = NULL,
  idents = NULL,
  extend.upstream = 0,
  extend.downstream = 0,
  colors = NULL,
  size = 10
)

Arguments

object: A Seurat object
region: A set of genomic coordinates to show. Can be a GRanges object, a string encoding a genomic position, a gene name, or a vector of strings describing the genomic coordinates or gene names to plot. If a gene name is supplied, annotations must be present in the assay.
features: A vector of features present in another assay to plot alongside accessibility tracks (for example, gene names).
links: Display links
ranges.group.by: Grouping variable to color ranges by. Must be a variable present in the metadata stored in the ranges genomic ranges. If NULL, do not color by any variable.
peaks: Display peaks
bigwig: List of bigWig file paths to plot data from. Files can be remotely hosted. The name of each element in the list will determine the y-axis label given to the track.
region.highlight: Region to highlight on the plot. Should be a GRanges object containing the coordinates to highlight. By default, regions will be highlighted in grey. To change the color of the highlighting, include a metadata column in the GRanges object named "color" containing the color to use for each region.
idents: Which identities to include in the plot. Default is all identities.
extend.upstream: Number of bases to extend the region upstream.
extend.downstream: Number of bases to extend the region downstream.
colors: A list of colors to fill different genomic ranges
size: The font size