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.

Value

Returns a ggplot object

Examples

# \donttest{
AnnotationPlot(object = atac_small, region = c("chr1-29554-39554"))
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the Signac package.
#>   Please report the issue at <https://github.com/stuart-lab/signac/issues>.
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the Signac package.
#>   Please report the issue at <https://github.com/stuart-lab/signac/issues>.

# }