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    <div class="page-header">
    <h1>Graph kernel methods for graph structure/topology comparisons</h1>
    <small class="dont-index">Source: <a href="https://github.com/alexyermanos/Platypus/tree/masterR/AntibodyForests_kernels.R" class="external-link"><code>R/AntibodyForests_kernels.R</code></a></small>
    <div class="hidden name"><code>AntibodyForests_kernels.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Performs graph structural comparisons using graph kernel-based method. Currently available kernel methods include: the Weisfeiler-Lehman kernel, the graphlet kernel, and the random walk kernel.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">AntibodyForests_kernels</span><span class="op">(</span></span>
<span>  <span class="va">trees</span>,</span>
<span>  <span class="va">graph.type</span>,</span>
<span>  <span class="va">kernel.method</span>,</span>
<span>  <span class="va">additional.param</span>,</span>
<span>  <span class="va">max.networks</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>trees</dt>
<dd><p>(nested) list of AntibodyForests objects, as obtained from the AntibodyForests function, to be compared.</p></dd>


<dt>graph.type</dt>
<dd><p>string - 'tree' will use the usual output of the AntibodyForests function (tree graphs), 'heterogeneous' will use the output of the AntibodyForests_heterogeneous function (bipartite networks for both cells and sequences).</p></dd>


<dt>kernel.method</dt>
<dd><p>string - kernel method to be used, as implemented in the 'graphkernels' R package. 'weisfeiler_lehman' for the Weisfeiler-Lehman kernel, 'graphlet, and 'random_walk'.</p></dd>


<dt>additional.param</dt>
<dd><p>integer - additional kernel options/parameters (e.g., kernel iterations for the Weisfeiler-Lehman kernel).</p></dd>


<dt>max.networks</dt>
<dd><p>integer - maximum number of networks to be compared (will pick the networks with the most number of cells first).</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>Heatmap of the graph kernel values.</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span><span class="fu">AntibodyForests_kernels</span><span class="op">(</span><span class="va">trees</span>, graph.type <span class="op">=</span> <span class="st">'tree'</span>,</span></span>
<span class="r-in"><span>kernel.method <span class="op">=</span> <span class="st">'weisfeiler_lehman'</span>,</span></span>
<span class="r-in"><span>additional.params <span class="op">=</span> <span class="fl">10</span>, max.networks <span class="op">=</span> <span class="fl">50</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
</code></pre></div>
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