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Plot ATAC fragment lengths

Source: R/ATACFragmentPlot.R
ATACFragmentPlot.Rd

Plot fragment lengths in an explicitly selected genomic region using Signac::FragmentHistogram(). This is a regional diagnostic, not a whole-library fragment-length estimate.

Usage

ATACFragmentPlot(
  object,
  region,
  assay = NULL,
  group.by = NULL,
  cells = NULL,
  log.scale = FALSE,
  ...
)

Arguments

object

A Seurat object containing a ChromatinAssay.

region

Genomic region(s), as a GRanges or strings accepted by Signac. Required explicitly to avoid silently assuming chromosome naming or genome.

assay

Name of the ChromatinAssay; defaults to the active assay.

group.by

One metadata column used for grouping, or NULL for identities.

cells

Cell names in the selected assay; NULL uses all assay cells.

log.scale

Whether to use a logarithmic count axis.

...

Arguments passed to other functions.

Value

A ggplot object. The input object is not modified.

Details

Requires local bgzip fragment files with a .tbi or .csi index and explicit cell/barcode mappings. The histogram counts fragment records, not column-five read multiplicities, and displays lengths between 0 and 800 bp by default. As in Signac, a fragment returned for several query intervals can contribute more than once; use a single region for an unambiguous regional histogram.

See also

RunATACQC()

Examples

if (FALSE) { # \dontrun{
ATACFragmentPlot(object, region = "chr1-1-2000000", assay = "peaks")
} # }