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<!DOCTYPE html>
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<h1>Generate a 3D model from connector and/or tree node data</h1>
<small class="dont-index">Source: <a href="https://github.com/natverse/nat/blob/HEAD/R/interactive.R" class="external-link"><code>R/interactive.R</code></a></small>
<div class="hidden name"><code>make_model.Rd</code></div>
</div>
<div class="ref-description">
<p>Generate a mesh3d model based on points contained in a
neuronlist or neuron object, or another object that consists of 3D points.</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">make_model</span><span class="op">(</span>
<span class="va">x</span>,
substrate <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cable"</span>, <span class="st">"connectors"</span>, <span class="st">"both"</span><span class="op">)</span>,
alpha <span class="op">=</span> <span class="fl">30</span>,
auto.selection <span class="op">=</span> <span class="cn">TRUE</span>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>a neuronlist or neuron object, or another object that consists of 3D points</p></dd>
<dt>substrate</dt>
<dd><p>whether to make the model based on the 3D location of
connectors, neuron cable or both. Connectors are pre-synapse locations,
e.g. the pre-synapses of a <code>catmaidneuron</code> from the R package <code>catmaid</code>)</p></dd>
<dt>alpha</dt>
<dd><p>a single value or vector of values for alpha, fed to
<code><a href="https://rdrr.io/pkg/alphashape3d/man/ashape3d.html" class="external-link">alphashape3d::ashape3d</a></code>. Selection is subsequently interactive.</p></dd>
<dt>auto.selection</dt>
<dd><p>logical, whether or not to try and remove points based on interactively
choosing simple values for clustering.</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>A mesh3d object</p>
</div>
<div id="details">
<h2>Details</h2>
<p>Interactive function that allows a users to select points in 3D space from neuronlist/neuron objects,
or another object that is coercible in 3D points using <code><a href="xyzmatrix.html">xyzmatrix</a></code>. Points can first be automatically chosen, by
selecting an integer number of nearest neighbours to find for each point using <code><a href="https://rdrr.io/pkg/nabor/man/knn.html" class="external-link">nabor::knn</a></code>, and then a
maximum distance at which nodes can be part of a cluster. Next, <code><a href="select_points.html">select_points</a></code> is used to manually pick desired 3D
points. Lastly, <code><a href="https://rdrr.io/pkg/alphashape3d/man/ashape3d.html" class="external-link">alphashape3d::ashape3d</a></code> is used to create an alphashape around these points. The user can trial different values for
alpha until they get their desired result.</p>
</div>
<div id="see-also">
<h2>See also</h2>
<div class="dont-index"><p><code><a href="prune_online.html">prune_online</a></code></p></div>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span>
<span class="r-in"><span class="co"># Make a model based off of fly olfactory projection neuron arbours</span></span>
<span class="r-in"><span class="va">PN_blob</span> <span class="op">=</span> <span class="fu">make_model</span><span class="op">(</span><span class="va">Cell07PNs</span><span class="op">)</span></span>
<span class="r-in"><span class="op">}</span></span>
</code></pre></div>
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