PlotFootprint

A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.

Tim Stuart

Signac

Analysis of Single-Cell Chromatin Data

Avi Srivastava

Paul Hoffman

Rahul Satija

PlotFootprint function

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

Arguments

Plot motif footprinting results — PlotFootprint

<dl>

<dt>object</dt>
<dd>A Seurat object</dd>


<dt>features</dt>
<dd>A vector of features to plot</dd>


<dt>assay</dt>
<dd>Name of assay to use</dd>


<dt>group.by</dt>
<dd>A grouping variable</dd>


<dt>split.by</dt>
<dd>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.</dd>


<dt>idents</dt>
<dd>Set of identities to include in the plot</dd>


<dt>label</dt>
<dd>TRUE/FALSE value to control whether groups are labeled.</dd>


<dt>repel</dt>
<dd>Repel labels from each other</dd>


<dt>show.expected</dt>
<dd>Plot the expected Tn5 integration frequency below the
main footprint plot</dd>


<dt>normalization</dt>
<dd>Method to normalize for Tn5 DNA sequence bias. Options
are "subtract", "divide", or NULL to perform no bias correction.</dd>


<dt>label.top</dt>
<dd>Number of groups to label based on highest accessibility
in motif flanking region.</dd>


<dt>label.idents</dt>
<dd>Vector of identities to label. If supplied,
<code>label.top</code> will be ignored.</dd>

</dl>

PlotFootprint: Plot motif footprinting results

Description

Usage

Arguments