Signac (version 1.14.0)

TilePlot: 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
)

Value

Returns a ggplot object

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.

Examples

# \donttest{
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"))
# }