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    <h1>Genome Size vs. Protein Space</h1>
    <small class="dont-index">Source: <a href='https://github.com/HajkD/LTRpred/blob/master/R/plotProteinSpace.R'><code>R/plotProteinSpace.R</code></a></small>
    <div class="hidden name"><code>plotProteinSpace.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Compute and visualize the correlation between genome size vs. Protein Space.</p>
    </div>

    <pre class="usage"><span class='fu'>plotProteinSpace</span>(
  <span class='no'>genome.matrix</span>,
  <span class='kw'>cor.method</span> <span class='kw'>=</span> <span class='st'>"spearman"</span>,
  <span class='kw'>label.organism</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
  <span class='kw'>smooth.method</span> <span class='kw'>=</span> <span class='st'>"glm"</span>,
  <span class='kw'>se</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
  <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Protein coding gene length in Mega [bp]"</span>,
  <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Genome size in Mega [bp]"</span>,
  <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>""</span>,
  <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.3</span>,
  <span class='kw'>arrow_lab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
  <span class='kw'>cl.analysis</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
  <span class='kw'>cl.centers</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
  <span class='kw'>cl.method</span> <span class='kw'>=</span> <span class='st'>"euclidean"</span>,
  <span class='kw'>cl.nstart</span> <span class='kw'>=</span> <span class='fl'>100</span>,
  <span class='kw'>cl.iter.max</span> <span class='kw'>=</span> <span class='fl'>10000</span>,
  <span class='kw'>sim.matrix</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
  <span class='kw'>text.size</span> <span class='kw'>=</span> <span class='fl'>18</span>,
  <span class='kw'>label.size</span> <span class='kw'>=</span> <span class='fl'>3</span>,
  <span class='kw'>check.overlap</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>genome.matrix</th>
      <td><p>Genome matrix retruned by <code><a href='LTRpred.meta.html'>LTRpred.meta</a></code>.</p></td>
    </tr>
    <tr>
      <th>cor.method</th>
      <td><p>method to correlate genome size versus protein space.</p></td>
    </tr>
    <tr>
      <th>label.organism</th>
      <td><p>shall organism names be drawn in the figure?</p></td>
    </tr>
    <tr>
      <th>smooth.method</th>
      <td><p>method to add a smoothed conditional mean (see <code><a href='https://ggplot2.tidyverse.org/reference/geom_smooth.html'>ggplot2::geom_smooth()</a></code>).
Users can choose from <code>auto</code>, <code>glm</code>, <code>lm</code>, or <code>loess</code>. If no smoothing function shall be applied,
users can specify <code>smooth.method = 'NULL'</code>.</p></td>
    </tr>
    <tr>
      <th>se</th>
      <td><p>shall standard error of the smoothing model (grey area) be drawn or not.</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>main</th>
      <td><p>main text.</p></td>
    </tr>
    <tr>
      <th>alpha</th>
      <td><p>transparency of confidence interval of the smoothing function: between \[ 0,1 \].</p></td>
    </tr>
    <tr>
      <th>arrow_lab</th>
      <td><p>whether or not data points shall be labelled with arrows (ggrepel).</p></td>
    </tr>
    <tr>
      <th>cl.analysis</th>
      <td><p>logical value indicating whether or not cluster analysis of the <code>sim.matrix</code> returned by <code><a href='LTRpred.meta.html'>LTRpred.meta</a></code> shall be performed (see Details sections).</p></td>
    </tr>
    <tr>
      <th>cl.centers</th>
      <td><p>number of expected clusters or a set of initial (distinct) cluster centres.</p></td>
    </tr>
    <tr>
      <th>cl.method</th>
      <td><p>distance measure to perform cluster analysis. Options are <code>"euclidean"</code>, <code>"maximum"</code>, <code>"manhattan"</code>, <code>"canberra"</code>, <code>"binary"</code>, <code>"pearson"</code> , <code>"abspearson"</code> , <code>"abscorrelation"</code>, <code>"correlation"</code>, <code>"spearman"</code> or <code>"kendall"</code>.</p></td>
    </tr>
    <tr>
      <th>cl.nstart</th>
      <td><p>If <code>cl.centers</code> is a number, number of random sets that shall be chosen.</p></td>
    </tr>
    <tr>
      <th>cl.iter.max</th>
      <td><p>maximum number of iterations for cluster analysis.</p></td>
    </tr>
    <tr>
      <th>sim.matrix</th>
      <td><p>Similarity matrix retruned by <code><a href='LTRpred.meta.html'>LTRpred.meta</a></code>.</p></td>
    </tr>
    <tr>
      <th>text.size</th>
      <td><p>size of the labels in ggplot2 notation.</p></td>
    </tr>
    <tr>
      <th>label.size</th>
      <td><p>size of the dot-labels.</p></td>
    </tr>
    <tr>
      <th>check.overlap</th>
      <td><p>shall overlaps of labels be avoided or not.</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    <p>In the first step, users should have generated LTR retrotransposon annotations for several species using the
<code><a href='LTRpred.meta.html'>LTRpred.meta</a></code> function. The output of <code><a href='LTRpred.meta.html'>LTRpred.meta</a></code> is a folder storing the annotation files
for all species of input species. In addition, <code><a href='LTRpred.meta.html'>LTRpred.meta</a></code> generates two files: <code>*_SimilarityMatrix</code> and <code>*_GenomeInfo</code> .</p>

  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
    <h2>Contents</h2>
    <ul class="nav nav-pills nav-stacked">
      <li><a href="#arguments">Arguments</a></li>
      <li><a href="#details">Details</a></li>
    </ul>

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