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PlotFootprint

Plot motif footprinting results

Description

Plot motif footprinting results

Usage

PlotFootprint(
  object,
  features,
  assay = NULL,
  group.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
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.
Signac

Analysis of Single-Cell Chromatin Data

v1.2.1
MIT + file LICENSE
Authors
Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>), Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>), Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>), Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)
Initial release
2021-05-11

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