PlotFootprint: Plot motif footprinting results

In timoast/signac: Analysis of Single-Cell Chromatin Data

Plot motif footprinting results

Description

Plot motif footprinting results

Usage

PlotFootprint(
  object,
  features,
  assay = NULL,
  group.by = NULL,
  split.by = NULL,
  idents = NULL,
  label = TRUE,
  repel = TRUE,
  show.expected = TRUE,
  normalization = "subtract",
  label.top = 3,
  label.idents = NULL
)

Arguments

object	A Seurat object
features	A vector of features to plot
assay	Name of assay to use
group.by	A grouping variable
split.by	A metadata variable to split the plot by. For example, grouping by "celltype" and splitting by "batch" will create separate plots for each celltype and batch.
idents	Set of identities to include in the plot
label	TRUE/FALSE value to control whether groups are labeled.
repel	Repel labels from each other
show.expected	Plot the expected Tn5 integration frequency below the main footprint plot
normalization	Method to normalize for Tn5 DNA sequence bias. Options are "subtract", "divide", or NULL to perform no bias correction.
label.top	Number of groups to label based on highest accessibility in motif flanking region.
label.idents	Vector of identities to label. If supplied, label.top will be ignored.

timoast/signac documentation built on Aug. 23, 2024, 1:48 a.m.