cytof-data

AML10.node287

AML10.node287.rips

Arip

This data set contains 18 columns of protein expression values
 measured in 214 early monocyte cells using mass cytometry (CyTOF).

datasets

Visualizations to explain the results of a topological
data analysis. The goal of topological data analysis is to identify
persistent topological structures, such as loops (topological circles)
and voids (topological spheres), in data sets. The output of an
analysis using the 'TDA' package is a Rips diagram (named after the
mathematician Eliyahu Rips). The goal of 'RPointCloud' is to fill in
these holes in the data by providing tools to visualize the features
that help explain the structures found in the Rips diagram. See McGee
and colleagues (2024) <doi:10.1101/2024.05.16.593927>.

Kevin Coombes

RPointCloud

Visualizing Topological Loops and Voids

Kevin R. Coombes

Jake Reed

RB McGee

cytof-data function

Note that there are three distinct objects included in the data
 set: <code>AML10.node287</code>, <code>AML10,node287.rips</code>, and <code>Arip</code>.<dl>
 <dt><code>AML10.node287</code></dt>
<dd>A numerical data matrix with 214 rows
 (single cells) amd 18 columns (antibody-protein markers). Values
 were obtained using mass cytometry applied to a sample collected
 from a patient with acute myeloid leukemia (AML).</dd>
 
 <dt><code>AML10.node287.rips</code></dt>
<dd>This object is a
 "Rips diagram". It was produced by running the
 <code>ripsDiag</code> function from the <code>TDA</code> R
 package on the <code>AML10.node287</code> data matrix.</dd> <dt><code>Arip</code></dt>
<dd>This object is a "Rips diagram". It was produced
 by running the <code>ripsDiag</code> function from the
 <code>TDA</code> R package on the Euclidean distance matrix
 between the single cells.</dd> 
</dl>

Format

Kevin R. Coombes <a href="/link/krc%40silicovore.com?package=RPointCloud&version=0.8.0" data-mini-rdoc="RPointCloud::krc@silicovore.com">krc@silicovore.com</a>,
 RB McGee <a href="/link/mcgee%40sholycross.edu?package=RPointCloud&version=0.8.0" data-mini-rdoc="RPointCloud::mcgee@sholycross.edu">mcgee@sholycross.edu</a>,
 Jake Reed <a href="/link/hreed%40augusta.edu?package=RPointCloud&version=0.8.0" data-mini-rdoc="RPointCloud::hreed@augusta.edu">hreed@augusta.edu</a>

Author

CyTOF Data — cytof-data

Note that there are three distinct objects included in the data
 set: <code>AML10.node287</code>, <code>AML10,node287.rips</code>, and <code>Arip</code>.<dl>
 <dt><code>AML10.node287</code></dt>
<dd>A numerical data matrix with 214 rows
 (single cells) amd 18 columns (antibody-protein markers). Values
 were obtained using mass cytometry applied to a sample collected
 from a patient with acute myeloid leukemia (AML).</dd>
 
 <dt><code>AML10.node287.rips</code></dt>
<dd>This object is a
 "Rips diagram". It was produced by running the
 <code>ripsDiag</code> function from the <code>TDA</code> R
 package on the <code>AML10.node287</code> data matrix.</dd>

 <dt><code>Arip</code></dt>
<dd>This object is a "Rips diagram". It was produced
 by running the <code>ripsDiag</code> function from the
 <code>TDA</code> R package on the Euclidean distance matrix
 between the single cells.</dd>

 
</dl>

Kevin R. Coombes <a href='mailto:krc@silicovore.com'>krc@silicovore.com</a>,
 RB McGee <a href='mailto:mcgee@sholycross.edu'>mcgee@sholycross.edu</a>,
 Jake Reed <a href='mailto:hreed@augusta.edu'>hreed@augusta.edu</a>

cytof-data: CyTOF Data

Description

Usage

Arguments

Format

Author

References