FOV-class

A modern container for storing coordinates of spatially-resolved single
cells. Capable of storing multiple cell segmentation boundary masks.
Supports coordinates for spatially-resolved molecule (FISH) data.
Compatible with <code>SpatialImage</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> 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

FOV-class function

<dl>
<dt><code>molecules</code></dt>
<dd>(<code><a href="/link/list?package=SeuratObject&version=4.1.0" data-mini-rdoc="SeuratObject::list">list</a></code>) A named list of
<code>Molecules</code> objects defining
spatially-resolved molecular coordinates</dd></dl>
<dt><code>boundaries</code></dt>
<dd>(<code>[named]<a href="/link/list?package=SeuratObject&version=4.1.0" data-mini-rdoc="SeuratObject::list">list</a></code>
{<code>Segmentation</code>,
<code>Centroids</code>}) A named list of
<code>Segmentation</code> and
<code>Centroids</code> objects defining
spatially-resolved boundaries</dd>
<dt><code>assay</code></dt>
<dd>(<code><a href="/link/character%20%5B1L%5D?package=SeuratObject&version=4.1.0" data-mini-rdoc="SeuratObject::character [1L]">character [1L]</a></code>) A character
naming the associated assay of the spatial coordinates</dd>
<dt><code>key</code></dt>
<dd>(<code><a href="/link/character%20%5B1L%5D?package=SeuratObject&version=4.1.0" data-mini-rdoc="SeuratObject::character [1L]">character [1L]</a></code>) The key
for the spatial coordinates</dd>

Slots

The Field of View Object — FOV-class

<dl>
<dt><code>molecules</code></dt>
<dd>(<code><a href='https://rdrr.io/r/base/list.html'>list</a></code>) A named list of
<code>Molecules</code> objects defining
spatially-resolved molecular coordinates</dd>


<dt><code>boundaries</code></dt>
<dd>(<code>[named]<a href='https://rdrr.io/r/base/list.html'>list</a></code>
{<code>Segmentation</code>,
<code>Centroids</code>}) A named list of
<code>Segmentation</code> and
<code>Centroids</code> objects defining
spatially-resolved boundaries</dd>


<dt><code>assay</code></dt>
<dd>(<code><a href='https://rdrr.io/r/base/character.html'>character [1L]</a></code>) A character
naming the associated assay of the spatial coordinates</dd>


<dt><code>key</code></dt>
<dd>(<code><a href='https://rdrr.io/r/base/character.html'>character [1L]</a></code>) The key
for the spatial coordinates</dd>


</dl>

The Field of View Object

FOV-class: The Field of View Object

Description

Arguments

Slots

See Also