CreateFOV

CreateFOV.Centroids

CreateFOV.data.frame

CreateFOV.list

CreateFOV.Segmentation

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

CreateFOV function

<dl><dt>coords</dt>
<dd>Spatial coordinates</dd>
<dt>...</dt>
<dd>Arguments passed to other methods</dd>
<dt>molecules</dt>
<dd>A <code><a href="/link/data.frame?package=SeuratObject&version=5.2.0" data-mini-rdoc="SeuratObject::data.frame">data.frame</a></code> with spatially-resolved
molecule information or a
<code>Molecules</code> object</dd>
<dt>assay</dt>
<dd>Name of associated assay</dd>
<dt>key</dt>
<dd>Key for these spatial coordinates</dd>
<dt>misc</dt>
<dd>A list of miscellaneous information to store with the object</dd>
<dt>name</dt>
<dd>When <code>coords</code> is a <code><a href="/link/data.frame?package=SeuratObject&version=5.2.0" data-mini-rdoc="SeuratObject::data.frame">data.frame</a></code>,
<code>Centroids</code>, or
<code>Segmentation</code>, name
to store coordinates as</dd>
<dt>type</dt>
<dd>When providing a <code><a href="/link/data.frame?package=SeuratObject&version=5.2.0" data-mini-rdoc="SeuratObject::data.frame">data.frame</a></code>, specify if
the coordinates represent a cell segmentation or voxel centroids</dd>
<dt>nsides</dt>
<dd>The number of sides to represent cells/spots; pass
<code><a href="/link/Inf?package=SeuratObject&version=5.2.0" data-mini-rdoc="SeuratObject::Inf">Inf</a></code> to plot as circles</dd>
<dt>radius</dt>
<dd>Radius of shapes when plotting</dd>
<dt>theta</dt>
<dd>Angle to adjust shapes when plotting</dd></dl>

Arguments

Create Spatial Coordinates — CreateFOV

<dl>

<dt>coords</dt>
<dd>Spatial coordinates</dd>


<dt>...</dt>
<dd>Arguments passed to other methods</dd>


<dt>molecules</dt>
<dd>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with spatially-resolved
molecule information or a
<code>Molecules</code> object</dd>


<dt>assay</dt>
<dd>Name of associated assay</dd>


<dt>key</dt>
<dd>Key for these spatial coordinates</dd>


<dt>misc</dt>
<dd>A list of miscellaneous information to store with the object</dd>


<dt>name</dt>
<dd>When <code>coords</code> is a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code>,
<code>Centroids</code>, or
<code>Segmentation</code>, name
to store coordinates as</dd>


<dt>type</dt>
<dd>When providing a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code>, specify if
the coordinates represent a cell segmentation or voxel centroids</dd>


<dt>nsides</dt>
<dd>The number of sides to represent cells/spots; pass
<code><a href='https://rdrr.io/r/base/is.finite.html'>Inf</a></code> to plot as circles</dd>


<dt>radius</dt>
<dd>Radius of shapes when plotting</dd>


<dt>theta</dt>
<dd>Angle to adjust shapes when plotting</dd>

</dl>

Create Spatial Coordinates

CreateFOV: Create Spatial Coordinates

Description

Usage

Value

Arguments

See Also