VisiumV1-class

VisiumV1

The VisiumV1 class represents spatial information from the 10X Genomics Visium
platform

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. 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>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Paul Hoffman

Seurat

Tools for Single Cell Genomics

Andrew Butler

Saket Choudhary

Charlotte Darby

Jeff Farrell

Isabella Grabski

Christoph Hafemeister

Yuhan Hao

Austin Hartman

Jaison Jain

Longda Jiang

Madeline Kowalski

Skylar Li

Gesmira Molla

Efthymia Papalexi

Patrick Roelli

Rahul Satija

Karthik Shekhar

Avi Srivastava

Tim Stuart

Kristof Torkenczy

Shiwei Zheng

Satija Lab and Collaborators 

VisiumV1-class function

<dl>
<dt><code>image</code></dt>
<dd>A three-dimensional array with PNG image data, see
<code><a href="/link/readPNG?package=Seurat&version=5.0.3" data-mini-rdoc="Seurat::readPNG">readPNG</a></code> for more details</dd></dl>
<dt><code>scale.factors</code></dt>
<dd>An object of class <code>scalefactors</code>; see
<code>scalefactors</code> for more information</dd>
<dt><code>coordinates</code></dt>
<dd>A data frame with tissue coordinate information</dd>
<dt><code>spot.radius</code></dt>
<dd>Single numeric value giving the radius of the spots</dd>

Slots

The VisiumV1 class — VisiumV1-class

<dl>
<dt><code>image</code></dt>
<dd>A three-dimensional array with PNG image data, see
<code><a href='https://rdrr.io/pkg/png/man/readPNG.html'>readPNG</a></code> for more details</dd>


<dt><code>scale.factors</code></dt>
<dd>An object of class <code>scalefactors</code>; see
<code>scalefactors</code> for more information</dd>


<dt><code>coordinates</code></dt>
<dd>A data frame with tissue coordinate information</dd>


<dt><code>spot.radius</code></dt>
<dd>Single numeric value giving the radius of the spots</dd>


</dl>

The VisiumV1 class

VisiumV1-class: The VisiumV1 class

Description

Arguments

Slots