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<title>MA-plot from base means and log fold changes — degMA • DEGreport</title>


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    <h1>MA-plot from base means and log fold changes</h1>
    
    <div class="hidden name"><code>degMA.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>MA-plot addaptation to show the shrinking effect.</p>
    </div>

    <pre class="usage"><span class='fu'>degMA</span>(<span class='no'>results</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>label_points</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
  <span class='kw'>label_column</span> <span class='kw'>=</span> <span class='st'>"symbol"</span>, <span class='kw'>limit</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>diff</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
  <span class='kw'>correlation</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>results</th>
      <td><p><a href='DEGSet.html'>DEGSet</a> class.</p></td>
    </tr>
    <tr>
      <th>title</th>
      <td><p><em>Optional</em>. Plot title.</p></td>
    </tr>
    <tr>
      <th>label_points</th>
      <td><p>Optionally label these particular points.</p></td>
    </tr>
    <tr>
      <th>label_column</th>
      <td><p>Match label_points to this column in the results.</p></td>
    </tr>
    <tr>
      <th>limit</th>
      <td><p>Absolute maximum to plot on the log2FoldChange.</p></td>
    </tr>
    <tr>
      <th>diff</th>
      <td><p>Minimum difference between logFoldChange before and
after shrinking.</p></td>
    </tr>
    <tr>
      <th>raw</th>
      <td><p>Whether to plot just the unshrunken log2FC.</p></td>
    </tr>
    <tr>
      <th>correlation</th>
      <td><p>Whether to plot the correlation of the two logFCs.</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>MA-plot ggplot.</p>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>DESeq2</span>)
<span class='no'>dds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/DESeq2/man/makeExampleDESeqDataSet.html'>makeExampleDESeqDataSet</a></span>(<span class='kw'>betaSD</span><span class='kw'>=</span><span class='fl'>1</span>)
<span class='no'>dds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/DESeq2/man/DESeq.html'>DESeq</a></span>(<span class='no'>dds</span>)</div><div class='output co'>#&gt; <span class='message'>estimating size factors</span></div><div class='output co'>#&gt; <span class='message'>estimating dispersions</span></div><div class='output co'>#&gt; <span class='message'>gene-wise dispersion estimates</span></div><div class='output co'>#&gt; <span class='message'>mean-dispersion relationship</span></div><div class='output co'>#&gt; <span class='message'>final dispersion estimates</span></div><div class='output co'>#&gt; <span class='message'>fitting model and testing</span></div><div class='input'><span class='no'>res</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='degComps.html'>degComps</a></span>(<span class='no'>dds</span>, <span class='kw'>contrast</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"condition_B_vs_A"</span>))</div><div class='output co'>#&gt; <span class='message'>Doing 1 element(s).</span></div><div class='output co'>#&gt; <span class='message'>Doing results() for each element.</span></div><div class='output co'>#&gt; <span class='message'>Doing lcfSrink() for each element.</span></div><div class='output co'>#&gt; <span class='message'>using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).</span>
#&gt; <span class='message'></span>
#&gt; <span class='message'>Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.</span>
#&gt; <span class='message'>See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.</span>
#&gt; <span class='message'>Reference: https://doi.org/10.1093/bioinformatics/bty895</span></div><div class='input'><span class='fu'>degMA</span>(<span class='no'>res</span>)</div><div class='img'><img src='degMA-1.png' alt='' width='700' height='433' /></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="#value">Value</a></li>
      <li><a href="#examples">Examples</a></li>
    </ul>

    <h2>Author</h2>
    <p>Victor Barrera</p>
<p>Rory Kirchner</p>
<p>Lorena Pantano</p>
  </div>
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