graphMatrix

methods

Compared with the similar graph embedding method such as Laplacian Eigenmaps, 'Vicus' can exploit more local structures of graph data. For the details of the methods, see the reference section of 'GitHub' README.md <https://github.com/rikenbit/Vicus>.

Koki Tsuyuzaki

Vicus

Exploiting Local Structures to Improve Network-Based Analysis of
Biological Data

graphMatrix function

<dl> <dt>X</dt>
<dd>A numeric matrix (n times p).</dd> <dt>algorithm</dt>
<dd>Algorithm to construct a graph matrix. Vicus matrix (Vicus), Graph Laplacian matrix (LEM), and Hessian Locally Linear Embedding matrix (HLLE) are available (Default: "Vicus").</dd> <dt>K</dt>
<dd>The number of neighborhoods to construct a graph matrix (Default: 10).</dd> <dt>alpha</dt>
<dd>An optional parameter for Vicus (Default: 0.9).</dd> <dt>ndim</dt>
<dd>The number of lower dimension to embed the graph (Default: 2).</dd></dl>

Arguments

Author

Graph Laplacian type matrix — graphMatrix

<dl>

 <dt>X</dt>
<dd>A numeric matrix (n times p).</dd>

 <dt>algorithm</dt>
<dd>Algorithm to construct a graph matrix. Vicus matrix (Vicus), Graph Laplacian matrix (LEM), and Hessian Locally Linear Embedding matrix (HLLE) are available (Default: "Vicus").</dd>

 <dt>K</dt>
<dd>The number of neighborhoods to construct a graph matrix (Default: 10).</dd>

 <dt>alpha</dt>
<dd>An optional parameter for Vicus (Default: 0.9).</dd>

 <dt>ndim</dt>
<dd>The number of lower dimension to embed the graph (Default: 2).</dd>

</dl>

graphMatrix: Graph Laplacian type matrix

Description

Usage

Value

Arguments

Author

See Also

Examples