TilePlot: Plot integration sites per cell

In timoast/signac: Analysis of Single-Cell Chromatin Data

Plot integration sites per cell

Description

Plots the presence/absence of Tn5 integration sites for each cell within a genomic region.

Usage

TilePlot(
  object,
  region,
  sep = c("-", "-"),
  tile.size = 100,
  tile.cells = 100,
  extend.upstream = 0,
  extend.downstream = 0,
  assay = NULL,
  cells = NULL,
  group.by = NULL,
  order.by = "total",
  idents = NULL
)

Arguments

object	A Seurat object
region	A set of genomic coordinates to show. Can be a GRanges object, a string encoding a genomic position, a gene name, or a vector of strings describing the genomic coordinates or gene names to plot. If a gene name is supplied, annotations must be present in the assay.
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.
tile.size	Size of the sliding window for per-cell fragment tile plot
tile.cells	Number of cells to display fragment information for in tile plot.
extend.upstream	Number of bases to extend the region upstream.
extend.downstream	Number of bases to extend the region downstream.
assay	Name of assay to use
cells	Which cells to plot. Default all cells
group.by	Name of grouping variable to group cells by. If NULL, use the current cell identities
order.by	Option for determining how cells are chosen from each group. Options are "total" or "random". "total" will select the top cells based on total number of fragments in the region, "random" will select randomly.
idents	List of cell identities to include in the plot. If NULL, use all identities.

Value

Returns a ggplot object

Examples

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
fragments <- CreateFragmentObject(
  path = fpath,
  cells = colnames(atac_small),
  validate.fragments = FALSE
)
Fragments(atac_small) <- fragments
TilePlot(object = atac_small, region = c("chr1-713500-714500"))

timoast/signac documentation built on Aug. 23, 2024, 1:48 a.m.