Skip to contents

Plot ATAC TSS enrichment profiles

Source: R/ATACTSSPlot.R
ATACTSSPlot.Rd

Plot previously computed per-position TSS enrichment with Signac::TSSPlot(). A scalar TSS enrichment score alone is insufficient.

Usage

ATACTSSPlot(object, assay = NULL, group.by = NULL, idents = NULL, cells = NULL)

Arguments

object

A Seurat object containing a ChromatinAssay.

assay

Name of the ChromatinAssay; defaults to the active assay.

group.by

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

idents

Group labels to retain, or NULL for all groups.

cells

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

Value

A ggplot object. The input object is not modified.

Details

First calculate positional enrichment with Signac::TSSEnrichment(..., fast = FALSE) or RunATACQC(..., tss.positions = tss, fast = FALSE). Supplying explicit TSS positions to RunATACQC forces recalculation even if imported scores exist. Use TSS coordinates from the matching reference and recompute positional enrichment after changing reference coordinates or preprocessing. This function never silently recomputes enrichment or invents a curve from scalar scores. Only cells in the selected assay are included. Signac 1.17 marks TSSPlot deprecated; any upstream lifecycle warning is retained.

See also

RunATACQC()

Examples

if (FALSE) { # \dontrun{
object <- RunATACQC(object, tss.positions = tss, fast = FALSE)
ATACTSSPlot(object, assay = "peaks", group.by = "celltype")
} # }