Signac (version 1.13.0)

FragmentHistogram: 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,
  ...
)

Value

Returns a ggplot object

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

Examples

# \donttest{
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")
# }