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<title>Plot the width distribution of putative LTR transposons — plot_ltrwidth_individual • LTRpred</title>


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(measured in LTR similarity) and the width of the corresponding LTR retrotransposon (the complete sequence) or the width of the left LTR element." />
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    <h1>Plot the width distribution of putative LTR transposons</h1>
    <small class="dont-index">Source: <a href='https://github.com/HajkD/LTRpred/blob/master/R/plot_ltrwidth_individual.R'><code>R/plot_ltrwidth_individual.R</code></a></small>
    <div class="hidden name"><code>plot_ltrwidth_individual.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Visualize the correlation between LTR transposon age
(measured in LTR similarity) and the width of the corresponding LTR retrotransposon (the complete sequence) or the width of the left LTR element.</p>
    </div>

    <pre class="usage"><span class='fu'>plot_ltrwidth_individual</span>(
  <span class='no'>data</span>,
  <span class='kw'>element.type</span> <span class='kw'>=</span> <span class='st'>"full_retrotransposon"</span>,
  <span class='kw'>plot.type</span> <span class='kw'>=</span> <span class='st'>"boxplot"</span>,
  <span class='kw'>similarity.bin</span> <span class='kw'>=</span> <span class='fl'>2</span>,
  <span class='kw'>min.sim</span> <span class='kw'>=</span> <span class='fl'>70</span>,
  <span class='kw'>quality.filter</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
  <span class='kw'>n.orfs</span> <span class='kw'>=</span> <span class='fl'>0</span>,
  <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"LTR % Similarity"</span>,
  <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"LTR Retrotransposon length in bp"</span>,
  <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>""</span>,
  <span class='kw'>legend.title</span> <span class='kw'>=</span> <span class='st'>"Similarity between LTRs"</span>,
  <span class='kw'>y.ticks</span> <span class='kw'>=</span> <span class='fl'>10</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>data</th>
      <td><p>the <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> generated by <code><a href='LTRpred.html'>LTRpred</a></code>.</p></td>
    </tr>
    <tr>
      <th>element.type</th>
      <td><p>which width shall be visualized. Full retrotransposon width or only LTR element width: 
choose <code>element.type = "full_retrotransposon"</code> or <code>element.type = "ltr_element"</code>. 
In case <code>element.type = "ltr_element"</code> is chosen then the width of the left LTR element is 
used to visualize width vs. seq. similarity between the LTRs.</p></td>
    </tr>
    <tr>
      <th>plot.type</th>
      <td><p>type of visualization: either <code>plot.type = "boxplot"</code> or <code>plot.type = "violin"</code>.</p></td>
    </tr>
    <tr>
      <th>similarity.bin</th>
      <td><p>resolution of similarity binning. E.g. binning 98%-100% into 0.5% intervals would be <code>similarity.bin = 0.5</code>.</p></td>
    </tr>
    <tr>
      <th>min.sim</th>
      <td><p>minimum similarity between LTRs that can shall be considered for visualization.</p></td>
    </tr>
    <tr>
      <th>quality.filter</th>
      <td><p>shall false positives be filtered out as much as possible or not. See Description for details.</p></td>
    </tr>
    <tr>
      <th>n.orfs</th>
      <td><p>minimum number of ORFs detected in the putative LTR transposon.</p></td>
    </tr>
    <tr>
      <th>xlab</th>
      <td><p>label of x-axis.</p></td>
    </tr>
    <tr>
      <th>ylab</th>
      <td><p>label of y-axis.</p></td>
    </tr>
    <tr>
      <th>main</th>
      <td><p>title label.</p></td>
    </tr>
    <tr>
      <th>legend.title</th>
      <td><p>title of legend.</p></td>
    </tr>
    <tr>
      <th>y.ticks</th>
      <td><p>number of ticks at the y-axis. Default is <code>y.ticks = 10</code>.</p></td>
    </tr>
    </table>

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

    <p>This function visualizes the correlation between LTR transposon age
(measured in LTR similarity) and the width of the corresponding LTR retrotransposon (the complete sequence) or the width of the left LTR element. Using this visualization approach, different classes of LTR retrotransposons can be detected due to their width and age correlation.</p>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># run LTRpred for A. thaliana</span>
<span class='no'>Ath.Pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='LTRpred.html'>LTRpred</a></span>(<span class='kw'>genome.file</span> <span class='kw'>=</span> <span class='st'>"TAIR10_chr_all.fas"</span>,
                    <span class='kw'>trnas</span>       <span class='kw'>=</span> <span class='st'>"plantRNA_Arabidopsis.fsa"</span>,
                    <span class='kw'>hmms</span>        <span class='kw'>=</span> <span class='st'>"hmm_*"</span>)

<span class='co'># visualize the collelation between LTR transposon age and width</span>
<span class='co'># of predicted  A. thaliana LTR retrotransposons</span>
<span class='fu'>plot_ltrwidth_individual</span>(<span class='no'>Ath.Pred</span>, <span class='kw'>plot.type</span> <span class='kw'>=</span> <span class='st'>"violin"</span>)

<span class='co'># visualize the collelation between LTR retrotransposon age and width</span>
<span class='co'># of predicted  A. thaliana LTR element</span>
<span class='fu'>plot_ltrwidth_individual</span>(<span class='no'>Ath.Pred</span>, <span class='kw'>element.type</span> <span class='kw'>=</span> <span class='st'>"full_retrotransposon"</span>)
}</div></pre>
  </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>
      <li><a href="#examples">Examples</a></li>
    </ul>

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