ISpatialDimPlot

Visualize clusters spatially and interactively

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

Christoph Hafemeister

Yuhan Hao

Austin Hartman

Jaison Jain

Madeline Kowalski

Efthymia Papalexi

Patrick Roelli

Rahul Satija

Karthik Shekhar

Avi Srivastava

Tim Stuart

Kristof Torkenczy

Shiwei Zheng

Satija Lab and Collaborators 

ISpatialDimPlot function

<dl><dt>object</dt>
<dd>Seurat object</dd>
<dt>image</dt>
<dd>Name of the image to use in the plot</dd>
<dt>group.by</dt>
<dd>Name of one or more metadata columns to group (color) cells by
(for example, orig.ident); pass 'ident' to group by identity class</dd>
<dt>alpha</dt>
<dd>Controls opacity of spots. Provide as a vector specifying the
min and max for SpatialFeaturePlot. For SpatialDimPlot, provide a single
alpha value for each plot.</dd></dl>

Arguments

Visualize clusters spatially and interactively — ISpatialDimPlot

<dl>

<dt>object</dt>
<dd>Seurat object</dd>


<dt>image</dt>
<dd>Name of the image to use in the plot</dd>


<dt>group.by</dt>
<dd>Name of one or more metadata columns to group (color) cells by
(for example, orig.ident); pass 'ident' to group by identity class</dd>


<dt>alpha</dt>
<dd>Controls opacity of spots. Provide as a vector specifying the
min and max for SpatialFeaturePlot. For SpatialDimPlot, provide a single
alpha value for each plot.</dd>

</dl>

Visualize clusters spatially and interactively

ISpatialDimPlot: Visualize clusters spatially and interactively

Description

Usage

Value

Arguments