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>,
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

FOV-class function

<dl>
<dt><code>molecules</code></dt>
<dd>A named list of
<code>Molecules</code> objects defining
spatially-resolved molecular coordinates</dd></dl>
<dt><code>boundaries</code></dt>
<dd>A named list of
<code>Segmentation</code> and
<code>Centroids</code> objects defining
spatially-resolved boundaries</dd>
<dt><code>coords_x_orientation</code></dt>
<dd>A character indicating which axis 
<code>x</code> coordinates are associated with in spatial plots. 
Currently only applies to Visium objects. Ensures consistency in 
plotting spatial data across versions, as objects prior to the 
addition of this slot had <code>x</code> coordinates mapped to the vertical axis.</dd>
<dt><code>assay</code></dt>
<dd>A character naming the associated assay
of the spatial coordinates</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 Field of View Object — FOV-class

<dl>
<dt><code>molecules</code></dt>
<dd>A named list of
<code>Molecules</code> objects defining
spatially-resolved molecular coordinates</dd>


<dt><code>boundaries</code></dt>
<dd>A named list of
<code>Segmentation</code> and
<code>Centroids</code> objects defining
spatially-resolved boundaries</dd>


<dt><code>coords_x_orientation</code></dt>
<dd>A character indicating which axis 
<code>x</code> coordinates are associated with in spatial plots. 
Currently only applies to Visium objects. Ensures consistency in 
plotting spatial data across versions, as objects prior to the 
addition of this slot had <code>x</code> coordinates mapped to the vertical axis.</dd>


<dt><code>assay</code></dt>
<dd>A character naming the associated assay
of the spatial coordinates</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 Field of View Object

FOV-class: The Field of View Object

Description

Arguments

Slots

See Also