Segmentation-class

A container for cell segmentation boundaries.
Inherits from <code><a href="https://edzer.github.io/sp/reference/SpatialPolygons-class.html">SpatialPolygons</a></code>.
Supports storing boundaries in objects of class <code><a href="https://r-spatial.github.io/sf/reference/sf.html">sf</a></code>.

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

Anagha Shenoy

Jeff Farrell

Shiwei Zheng

Christoph Hafemeister

Patrick Roelli

Segmentation-class function

<dl>
<dt><code>sf.data</code></dt>
<dd>Segmentation boundaries in <code><a href="https://r-spatial.github.io/sf/reference/sf.html">sf</a></code> format</dd></dl>
<dt><code>compact</code></dt>
<dd>Logical indicating whether or not the object only stores 
segmentation information in the <code>sf.data</code> slot, rather than also in the
standard <code>SpatialPolygons</code> slots, to save memory and processing time.
Currently only relevant for Visium data.</dd>

Slots

A container for cell segmentation boundaries.
Inherits from <code><a href='https://edzer.github.io/sp/reference/SpatialPolygons-class.html'>SpatialPolygons</a></code>.
Supports storing boundaries in objects of class <code><a href='https://r-spatial.github.io/sf/reference/sf.html'>sf</a></code>.

The Segmentation Class — Segmentation-class

<dl>
<dt><code>sf.data</code></dt>
<dd>Segmentation boundaries in <code><a href='https://r-spatial.github.io/sf/reference/sf.html'>sf</a></code> format</dd>


<dt><code>compact</code></dt>
<dd>Logical indicating whether or not the object only stores 
segmentation information in the <code>sf.data</code> slot, rather than also in the
standard <code>SpatialPolygons</code> slots, to save memory and processing time.
Currently only relevant for Visium data.</dd>


</dl>

The <code>Segmentation</code> Class

Segmentation-class: The `Segmentation` Class

Description

Arguments

Slots

See Also