cluster_mat

Cluster Matrix Rows in Annotated Heatmaps

internal

Provides a framework to perform Non-negative Matrix
Factorization (NMF). The package implements a set of already published algorithms
and seeding methods, and provides a framework to test, develop and plug
new/custom algorithms. Most of the built-in algorithms have been optimized
in C++, and the main interface function provides an easy way of performing
parallel computations on multicore machines.

Nicolas Sauwen

Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)

Renaud Gaujoux

Cathal Seoighe

cluster_mat function

<dl> <dt>mat</dt>
<dd>original input matrix that has already been
 appropriately subset in the caller function
 (<code>aheatmap</code>)</dd>
 <dt>param</dt>
<dd>clustering specifications</dd>
 <dt>distfun</dt>
<dd>Default distance method/function</dd>
 <dt>hclustfun</dt>
<dd>Default clustering (linkage)
 method/function</dd>
 <dt>reorderfun</dt>
<dd>Default reordering function</dd>
 <dt>na.rm</dt>
<dd>Logical that specifies if NA values should
 be removed</dd>
 <dt>subset</dt>
<dd>index (integer) vector specifying the
 subset indexes used to subset mat. This is required to be
 able to return the original indexes.</dd></dl>

Arguments

Cluster Matrix Rows in Annotated Heatmaps — cluster_mat

<dl>

 <dt>mat</dt>
<dd>original input matrix that has already been
 appropriately subset in the caller function
 (<code>aheatmap</code>)</dd>


 <dt>param</dt>
<dd>clustering specifications</dd>


 <dt>distfun</dt>
<dd>Default distance method/function</dd>


 <dt>hclustfun</dt>
<dd>Default clustering (linkage)
 method/function</dd>


 <dt>reorderfun</dt>
<dd>Default reordering function</dd>


 <dt>na.rm</dt>
<dd>Logical that specifies if NA values should
 be removed</dd>


 <dt>subset</dt>
<dd>index (integer) vector specifying the
 subset indexes used to subset mat. This is required to be
 able to return the original indexes.</dd>

</dl>

cluster_mat: Cluster Matrix Rows in Annotated Heatmaps

Description

Usage

Arguments