Plot gene annotations — AnnotationPlot • Signac

Display gene annotations in a given region of the genome.

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.

Returns a ggplot object

# \donttest{
AnnotationPlot(object = atac_small, region = c("chr1-29554-39554"))

# }