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<title>Plot inter species similarity between TEs (for the top 6 clusters) — plotMainInterSpeciesCluster • LTRpred</title>


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the similarity of TEs from different species for the top 6 clusters is being visualized." />
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    <h1>Plot inter species similarity between TEs (for the top 6 clusters)</h1>
    <small class="dont-index">Source: <a href='https://github.com/HajkD/LTRpred/blob/master/R/plotMainInterSpeciesCluster.R'><code>R/plotMainInterSpeciesCluster.R</code></a></small>
    <div class="hidden name"><code>plotMainInterSpeciesCluster.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>After clustering TE sequences across different species with <code><a href='CLUSTpred.html'>CLUSTpred</a></code>
the similarity of TEs from different species for the top 6 clusters is being visualized.</p>
    </div>

    <pre class="usage"><span class='fu'>plotMainInterSpeciesCluster</span>(
  <span class='no'>cluster.file</span>,
  <span class='kw'>top.n</span> <span class='kw'>=</span> <span class='fl'>6</span>,
  <span class='kw'>decreasing</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
  <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Species"</span>,
  <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"% Similarity to Reference"</span>,
  <span class='kw'>legend.title</span> <span class='kw'>=</span> <span class='st'>"Species"</span>
)</pre>

    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
    <table class="ref-arguments">
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>cluster.file</th>
      <td><p>a cluster file in <code>*.uc</code> format (imported with e.g. <code><a href='filter.uc.html'>filter.uc</a></code> and <code><a href='read.uc.html'>read.uc</a></code>).</p></td>
    </tr>
    <tr>
      <th>top.n</th>
      <td><p>number of top clustern that shall be visualized.</p></td>
    </tr>
    <tr>
      <th>decreasing</th>
      <td><p>shall clusters be shown by size in decreasing order?</p></td>
    </tr>
    <tr>
      <th>xlab</th>
      <td><p>x-axis label.</p></td>
    </tr>
    <tr>
      <th>ylab</th>
      <td><p>y-axis label.</p></td>
    </tr>
    <tr>
      <th>legend.title</th>
      <td><p>legend title text.</p></td>
    </tr>
    </table>


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    <h2>Contents</h2>
    <ul class="nav nav-pills nav-stacked">
      <li><a href="#arguments">Arguments</a></li>
    </ul>

    <h2>Author</h2>
    <p>Hajk-Georg Drost</p>
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