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<h1>Create volcano plot from log2FC and adjusted pvalues data frame</h1>
<div class="hidden name"><code>degVolcano.Rd</code></div>
</div>
<div class="ref-description">
<p>Create volcano plot from log2FC and adjusted pvalues data frame</p>
</div>
<pre class="usage"><span class='fu'>degVolcano</span>(<span class='no'>stats</span>, <span class='kw'>side</span> <span class='kw'>=</span> <span class='st'>"both"</span>,
<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Volcano Plot with Marginal Distributions"</span>,
<span class='kw'>pval.cutoff</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>lfc.cutoff</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>shade.colour</span> <span class='kw'>=</span> <span class='st'>"orange"</span>,
<span class='kw'>shade.alpha</span> <span class='kw'>=</span> <span class='fl'>0.25</span>, <span class='kw'>point.colour</span> <span class='kw'>=</span> <span class='st'>"gray"</span>, <span class='kw'>point.alpha</span> <span class='kw'>=</span> <span class='fl'>0.75</span>,
<span class='kw'>point.outline.colour</span> <span class='kw'>=</span> <span class='st'>"darkgray"</span>, <span class='kw'>line.colour</span> <span class='kw'>=</span> <span class='st'>"gray"</span>,
<span class='kw'>plot_text</span> <span class='kw'>=</span> <span class='kw'>NULL</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>stats</th>
<td><p>data.frame with two columns: logFC and Adjusted.Pvalue</p></td>
</tr>
<tr>
<th>side</th>
<td><p>plot UP, DOWN or BOTH de-regulated points</p></td>
</tr>
<tr>
<th>title</th>
<td><p>title for the figure</p></td>
</tr>
<tr>
<th>pval.cutoff</th>
<td><p>cutoff for the adjusted pvalue. Default 0.05</p></td>
</tr>
<tr>
<th>lfc.cutoff</th>
<td><p>cutoff for the log2FC. Default 1</p></td>
</tr>
<tr>
<th>shade.colour</th>
<td><p>background color. Default orange.</p></td>
</tr>
<tr>
<th>shade.alpha</th>
<td><p>transparency value. Default 0.25</p></td>
</tr>
<tr>
<th>point.colour</th>
<td><p>colours for points. Default gray</p></td>
</tr>
<tr>
<th>point.alpha</th>
<td><p>transparency for points. Default 0.75</p></td>
</tr>
<tr>
<th>point.outline.colour</th>
<td><p>Default darkgray</p></td>
</tr>
<tr>
<th>line.colour</th>
<td><p>Defaul gray</p></td>
</tr>
<tr>
<th>plot_text</th>
<td><p>data.frame with three columns: logFC, Pvalue, Gene name</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The function will plot volcano plot together
with density of the fold change and p-values on the top and the
right side of the volcano plot.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function was mainly developed by @jnhutchinson.</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'><-</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'><-</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'>#> <span class='message'>estimating size factors</span></div><div class='output co'>#> <span class='message'>estimating dispersions</span></div><div class='output co'>#> <span class='message'>gene-wise dispersion estimates</span></div><div class='output co'>#> <span class='message'>mean-dispersion relationship</span></div><div class='output co'>#> <span class='message'>final dispersion estimates</span></div><div class='output co'>#> <span class='message'>fitting model and testing</span></div><div class='input'><span class='no'>stats</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/DESeq2/man/results.html'>results</a></span>(<span class='no'>dds</span>)[,<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"log2FoldChange"</span>, <span class='st'>"padj"</span>)]
<span class='no'>stats</span><span class='kw'>[[</span><span class='st'>"name"</span>]] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/row.names.html'>row.names</a></span>(<span class='no'>stats</span>)
<span class='fu'>degVolcano</span>(<span class='no'>stats</span>, <span class='kw'>plot_text</span> <span class='kw'>=</span> <span class='no'>stats</span>[<span class='fl'>1</span>:<span class='fl'>10</span>,])</div><div class='output co'>#> <span class='warning'>Warning: Removed 1 rows containing missing values (geom_text_repel).</span></div><div class='img'><img src='degVolcano-1.png' alt='' width='700' height='433' /></div></pre>
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<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="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<h2>Author</h2>
<p>Lorena Pantano, John Hutchinson</p>
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