Plot linked genomic elements

Display links between pairs of genomic elements within a given region of the genome.

LinkPlot(
  object,
  region,
  assay = NULL,
  min.cutoff = 0,
  sep = c("-", "-"),
  extend.upstream = 0,
  extend.downstream = 0,
  scale.linewidth = FALSE
)

Arguments

object

A Seurat object

region

A genomic region to plot

assay

Name of assay to use. If NULL, use the default assay.

min.cutoff

Minimum absolute score for link to be 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.

scale.linewidth

Scale thickness of the line according to link score.

Value

Returns a ggplot object