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> for
more details.

Paul Hoffman

SeuratObject

Data Structures for Single Cell Data

Rahul Satija

Andrew Butler

Tim Stuart

Jeff Farrell

Shiwei Zheng

Christoph Hafemeister

Patrick Roelli

Yuhan Hao

DimReduc-class function

<dl class="dl-horizontal">
<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>key</code></dt><dd>Key for the <code>DimReduc</code>, must be alphanumeric characters
followed by an underscore</dd><dt><code>jackstraw</code></dt><dd>A <code><a rd-options="" href="/link/JackStrawData-class?package=SeuratObject&version=4.0.1" data-mini-rdoc="SeuratObject::JackStrawData-class">JackStrawData-class</a></code> object associated with
this <code>DimReduc</code></dd><dt><code>misc</code></dt><dd>Utility slot for storing additional data associated with the
<code>DimReduc</code> (e.g. the total variance of the PCA)</dd>

Slots

The Dimensional Reduction Class — DimReduc-class

The Dimensional Reduction Class

DimReduc-class: The Dimensional Reduction Class

Description

Arguments

Slots