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  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Flexible logoplot wrapper</h1>
    <small class="dont-index">Source: <a href="https://github.com/alexyermanos/Platypus/tree/masterR/VDJ_logoplot_vector.R" class="external-link"><code>R/VDJ_logoplot_vector.R</code></a></small>
    <div class="hidden name"><code>VDJ_logoplot_vector.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Plots a logoplot of the CDR3 aminoacid region</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">VDJ_logoplot_vector</span><span class="op">(</span><span class="va">cdr3.vector</span>, <span class="va">length_cdr3</span>, <span class="va">seq_type</span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>cdr3.vector</dt>
<dd><p>A character vector of aa sequences. This is to increase flexibility of this function. Such a sequence vector may be retrieved from the VDJ_analyse function output on a clonotype level or from the VDJ_GEX_matrix function output on a per cell level. Additionally, any length of sequence may be used (e.g. HCDR3 only or H and LCDR3 pasted together)</p></dd>


<dt>length_cdr3</dt>
<dd><p>Integer or character. Defaults to "auto". Sets the length of the CDR3 regions that are selected to be plotted. If set to auto, the most frequently appearing length in the vector will be used</p></dd>


<dt>seq_type</dt>
<dd><p>passed to ggseqlogo. Can be set to "aa", "dna", "rna" or "other"</p></dd>

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

<p>Returns the logo plot.</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">VDJ_logoplot_vector</span><span class="op">(</span></span></span>
<span class="r-in"><span>cdr3.vector <span class="op">=</span> <span class="fu">Platypus</span><span class="fu">::</span><span class="va"><a href="small_vgm.html">small_vgm</a></span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">VDJ_cdr3s_aa</span></span></span>
<span class="r-in"><span>,length_cdr3 <span class="op">=</span> <span class="st">"auto"</span>,seq_type <span class="op">=</span> <span class="st">"auto"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Returning logoplot based on 5 sequences of a total 34 input sequences</span>
<span class="r-plt img"><img src="VDJ_logoplot_vector-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
</code></pre></div>
    </div>
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