DimReduc-class

DimReduc

The DimReduc object stores a dimensionality reduction taken out in Seurat;
each DimReduc consists of a cell embeddings matrix, a feature loadings
matrix, and a projected feature loadings matrix.

Defines S4 classes for single-cell genomic data and associated
information, such as dimensionality reduction embeddings, nearest-neighbor
graphs, and spatially-resolved coordinates. Provides data access methods and
R-native hooks to ensure the Seurat object is familiar to other R users. See
Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>,
Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>,
and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>,
Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and
Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for
more details.

Paul Hoffman

SeuratObject

Data Structures for Single Cell Data

Rahul Satija

David Collins

Yuhan Hao

Austin Hartman

Gesmira Molla

Andrew Butler

Tim Stuart

Madeline Kowalski

Saket Choudhary

Skylar Li

Longda Jiang

Jeff Farrell

Shiwei Zheng

Christoph Hafemeister

Patrick Roelli

DimReduc-class function

<dl>
<dt><code>cell.embeddings</code></dt>
<dd>Cell embeddings matrix (required)</dd></dl>
<dt><code>feature.loadings</code></dt>
<dd>Feature loadings matrix (optional)</dd>
<dt><code>feature.loadings.projected</code></dt>
<dd>Projected feature loadings matrix (optional)</dd>
<dt><code>assay.used</code></dt>
<dd>Name of assay used to generate <code>DimReduc</code> object</dd>
<dt><code>global</code></dt>
<dd>Is this <code>DimReduc</code> global/persistent? If so, it will not be
removed when removing its associated assay</dd>
<dt><code>stdev</code></dt>
<dd>A vector of standard deviations</dd>
<dt><code>jackstraw</code></dt>
<dd>A <code>JackStrawData-class</code> object associated with
this <code>DimReduc</code></dd>
<dt><code>misc</code></dt>
<dd>A named list of unstructured miscellaneous data</dd>
<dt><code>key</code></dt>
<dd>A one-length character vector with the object's key; keys must
be one or more alphanumeric characters followed by an underscore
&#8220;<code>_</code>&#8221; (regex pattern
&#8220;<code>SeuratObject:::.KeyPattern()</code>&#8221;)</dd>

Slots

The Dimensional Reduction Class — DimReduc-class

<dl>
<dt><code>cell.embeddings</code></dt>
<dd>Cell embeddings matrix (required)</dd>


<dt><code>feature.loadings</code></dt>
<dd>Feature loadings matrix (optional)</dd>


<dt><code>feature.loadings.projected</code></dt>
<dd>Projected feature loadings matrix (optional)</dd>


<dt><code>assay.used</code></dt>
<dd>Name of assay used to generate <code>DimReduc</code> object</dd>


<dt><code>global</code></dt>
<dd>Is this <code>DimReduc</code> global/persistent? If so, it will not be
removed when removing its associated assay</dd>


<dt><code>stdev</code></dt>
<dd>A vector of standard deviations</dd>


<dt><code>jackstraw</code></dt>
<dd>A <code>JackStrawData-class</code> object associated with
this <code>DimReduc</code></dd>


<dt><code>misc</code></dt>
<dd>A named list of unstructured miscellaneous data</dd>


<dt><code>key</code></dt>
<dd>A one-length character vector with the object's key; keys must
be one or more alphanumeric characters followed by an underscore
&#8220;<code>_</code>&#8221; (regex pattern
&#8220;<code>SeuratObject:::.KeyPattern()</code>&#8221;)</dd>


</dl>

The Dimensional Reduction Class

DimReduc-class: The Dimensional Reduction Class

Description

Arguments

Slots

See Also