AnnotationPlot function

Plot gene annotations

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

Returns a ggplot object

Examples

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