FragmentHistogram: Plot fragment length histogram

In Signac: Analysis of Single-Cell Chromatin Data

Plot fragment length histogram

Description

Plot the frequency that fragments of different lengths are present for different groups of cells.

Usage

FragmentHistogram(
  object,
  assay = NULL,
  region = "chr1-1-2000000",
  group.by = NULL,
  cells = NULL,
  log.scale = FALSE,
  ...
)

Arguments

object	A Seurat object
assay	Which assay to use. Default is the active assay.
region	Genomic range to use. Default is fist two megabases of chromosome 1. Can be a GRanges object, a string, or a vector of strings.
group.by	Name of one or more metadata columns to group (color) the cells by. Default is the current cell identities
cells	Which cells to plot. Default all cells
log.scale	Display Y-axis on log scale. Default is FALSE.
...	Arguments passed to other functions

Value

Returns a ggplot object

Examples

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
Fragments(atac_small) <- CreateFragmentObject(
  path = fpath,
  cells = colnames(atac_small),
  validate.fragments = FALSE
)
FragmentHistogram(object = atac_small, region = "chr1-10245-780007")

Signac documentation built on Sept. 11, 2024, 9:30 p.m.