LinkPlot: Plot linked genomic elements

In Signac: Analysis of Single-Cell Chromatin Data

Plot linked genomic elements

Description

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

Usage

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

Signac documentation built on Nov. 8, 2023, 5:07 p.m.