WormTensor-class

S4 class used by as_worm_tensor.R, worm_membership.R, worm_clustering.R,
worm_evaluate.R, worm_visualize.R

A toolkit to detect clusters from distance matrices.
The distance matrices are assumed to be calculated between the cells of
multiple animals ('Caenorhabditis elegans') from input time-series matrices.
Some functions for generating distance matrices, performing clustering,
evaluating the clustering, and visualizing the results of clustering and
evaluation are available. We're also providing the download function to
retrieve the calculated distance matrices from
'figshare' <https://figshare.com>.

Kentaro Yamamoto

WormTensor

A Clustering Method for Time-Series Whole-Brain Activity Data of
'C. elegans'

Koki Tsuyuzaki

Itoshi Nikaido

WormTensor-class function

<dl>
<dt><code>dist_matrices</code></dt>
<dd>list</dd></dl>
<dt><code>n_animals</code></dt>
<dd>numeric</dd>
<dt><code>union_cellnames</code></dt>
<dd>character</dd>
<dt><code>n_union_cells</code></dt>
<dd>numeric</dd>
<dt><code>membership_tensor</code></dt>
<dd>Tensor</dd>
<dt><code>k</code></dt>
<dd>numeric</dd>
<dt><code>clustering_algorithm</code></dt>
<dd>character</dd>
<dt><code>clustering</code></dt>
<dd>numeric</dd>
<dt><code>weight</code></dt>
<dd>numeric</dd>
<dt><code>factor</code></dt>
<dd>matrix</dd>
<dt><code>consensus</code></dt>
<dd>matrix</dd>
<dt><code>eval</code></dt>
<dd>list</dd>
<dt><code>dimension_reduction_algorithm</code></dt>
<dd>character</dd>

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S4 class used by as_worm_tensor.R, worm_membership.R, worm_clustering.R,
worm_evaluate.R, worm_visualize.R — WormTensor-class

<dl>
<dt><code>dist_matrices</code></dt>
<dd>list</dd>


<dt><code>n_animals</code></dt>
<dd>numeric</dd>


<dt><code>union_cellnames</code></dt>
<dd>character</dd>


<dt><code>n_union_cells</code></dt>
<dd>numeric</dd>


<dt><code>membership_tensor</code></dt>
<dd>Tensor</dd>


<dt><code>k</code></dt>
<dd>numeric</dd>


<dt><code>clustering_algorithm</code></dt>
<dd>character</dd>


<dt><code>clustering</code></dt>
<dd>numeric</dd>


<dt><code>weight</code></dt>
<dd>numeric</dd>


<dt><code>factor</code></dt>
<dd>matrix</dd>


<dt><code>consensus</code></dt>
<dd>matrix</dd>


<dt><code>eval</code></dt>
<dd>list</dd>


<dt><code>dimension_reduction_algorithm</code></dt>
<dd>character</dd>


</dl>

WormTensor-class: S4 class used by as_worm_tensor.R, worm_membership.R, worm_clustering.R, worm_evaluate.R, worm_visualize.R

Description

Arguments

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