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    <h1>Get paired v gene heavy chain and light chain matrix on clonotype level. A v gene usage pheatmap can be obtain by p&lt;-pheatmap::pheatmap(vgu_matrix,show_colnames= T, main = "V Gene Usage"), where the vgu_matrix is the output of this function.</h1>
    <small class="dont-index">Source: <a href="https://github.com/alexyermanos/Platypus/tree/masterR/Echidna_other_functions.R" class="external-link"><code>R/Echidna_other_functions.R</code></a></small>
    <div class="hidden name"><code>get.vgu.matrix.Rd</code></div>
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    <div class="ref-description">
    <p>Get paired v gene heavy chain and light chain matrix on clonotype level. A v gene usage pheatmap can be obtain by p&lt;-pheatmap::pheatmap(vgu_matrix,show_colnames= T, main = "V Gene Usage"), where the vgu_matrix is the output of this function.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get.vgu.matrix</span><span class="op">(</span><span class="va">all.contig.annotations</span>, <span class="va">level</span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>all.contig.annotations</dt>
<dd><p>The dataframe "all_contig_annotation" from simulation output.</p></dd>


<dt>level</dt>
<dd><p>Can be "clone" or "cell". If "clone", the function will return paired v gene usage matrix on clonotype level. Otherwise it will return on cell level.</p></dd>

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

<p>a paired v gene heavy chain and light chain matrix on clonotype level.</p>
    </div>

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