DefaultDimReduc

Searches for <code>DimReducs</code> matching &#8220;umap&#8221;, &#8220;tsne&#8221;,
or &#8220;pca&#8221;, case-insensitive, and in that order. Priority given to
<code>DimReducs</code> matching the <code>DefaultAssay</code> or assay specified
(eg. &#8220;pca&#8221; for the default assay weights higher than &#8220;umap&#8221;
for a non-default assay)

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

DefaultDimReduc function

<dl><dt>object</dt>
<dd>A <code>Seurat</code> object</dd>
<dt>assay</dt>
<dd>Name of assay to use; defaults to the default assay of the object</dd></dl>

Arguments

Find the default DimReduc — DefaultDimReduc

<dl>

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


<dt>assay</dt>
<dd>Name of assay to use; defaults to the default assay of the object</dd>

</dl>

Find the default <code>DimReduc</code>

DefaultDimReduc: Find the default `DimReduc`

Description

Usage

Value

Arguments

Examples