RegionPlot

Plot fragment counts within a set of regions.

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

RegionPlot function

<dl><dt>object</dt>
<dd>A Seurat object</dd>
<dt>key</dt>
<dd>Name of key to pull data from. Stores the results from
<code>RegionMatrix</code></dd>
<dt>assay</dt>
<dd>Name of assay to use. If a list or vector of assay names is
given, data will be plotted from each assay. Note that all assays must
contain <code>RegionMatrix</code> results with the same key. Sorting will be 
defined by the first assay in the list</dd>
<dt>idents</dt>
<dd>Cell identities to include. Note that cells cannot be
regrouped, this will require re-running <code>RegionMatrix</code> to generate a 
new set of matrices</dd>
<dt>normalize</dt>
<dd>Normalize by number of cells in each group</dd>
<dt>upstream</dt>
<dd>Number of bases to include upstream of region. If NULL, use
all bases that were included in the <code>RegionMatrix</code> function call. Note
that this value cannot be larger than the value for <code>upstream</code> given in
the original <code>RegionMatrix</code> function call. If NULL, use parameters that
were given in the <code>RegionMatrix</code> function call</dd>
<dt>downstream</dt>
<dd>Number of bases to include downstream of region. See
documentation for <code>upstream</code></dd>
<dt>window</dt>
<dd>Smoothing window to apply</dd>
<dt>nrow</dt>
<dd>Number of rows to use when creating plot. If NULL, chosen
automatically by ggplot2</dd></dl>

Arguments

Region plot — RegionPlot

<dl>

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


<dt>key</dt>
<dd>Name of key to pull data from. Stores the results from
<code>RegionMatrix</code></dd>


<dt>assay</dt>
<dd>Name of assay to use. If a list or vector of assay names is
given, data will be plotted from each assay. Note that all assays must
contain <code>RegionMatrix</code> results with the same key. Sorting will be 
defined by the first assay in the list</dd>


<dt>idents</dt>
<dd>Cell identities to include. Note that cells cannot be
regrouped, this will require re-running <code>RegionMatrix</code> to generate a 
new set of matrices</dd>


<dt>normalize</dt>
<dd>Normalize by number of cells in each group</dd>


<dt>upstream</dt>
<dd>Number of bases to include upstream of region. If NULL, use
all bases that were included in the <code>RegionMatrix</code> function call. Note
that this value cannot be larger than the value for <code>upstream</code> given in
the original <code>RegionMatrix</code> function call. If NULL, use parameters that
were given in the <code>RegionMatrix</code> function call</dd>


<dt>downstream</dt>
<dd>Number of bases to include downstream of region. See
documentation for <code>upstream</code></dd>


<dt>window</dt>
<dd>Smoothing window to apply</dd>


<dt>nrow</dt>
<dd>Number of rows to use when creating plot. If NULL, chosen
automatically by ggplot2</dd>

</dl>

RegionPlot: Region plot

Description

Usage

Value

Arguments

See Also