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<h1>Plot top genes allowing more variables to color and shape points</h1>
<div class="hidden name"><code>degPlot.Rd</code></div>
</div>
<div class="ref-description">
<p>Plot top genes allowing more variables to color and shape points</p>
</div>
<pre class="usage"><span class='fu'>degPlot</span>(<span class='no'>dds</span>, <span class='no'>xs</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>9</span>, <span class='kw'>genes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>group</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>batch</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>metadata</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>ann</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"geneID"</span>, <span class='st'>"symbol"</span>),
<span class='kw'>slot</span> <span class='kw'>=</span> <span class='fl'>1L</span>, <span class='kw'>log2</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>xsLab</span> <span class='kw'>=</span> <span class='no'>xs</span>, <span class='kw'>ysLab</span> <span class='kw'>=</span> <span class='st'>"abundance"</span>,
<span class='kw'>color</span> <span class='kw'>=</span> <span class='st'>"black"</span>, <span class='kw'>groupLab</span> <span class='kw'>=</span> <span class='no'>group</span>, <span class='kw'>batchLab</span> <span class='kw'>=</span> <span class='no'>batch</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>dds</th>
<td><p><a href='https://rdrr.io/pkg/DESeq2/man/DESeqDataSet.html'>DESeq2::DESeqDataSet</a> object or SummarizedExperiment
or Matrix or data.frame. In case of a DESeqDataSet object, always
the normalized expression will be used
from <code>counts(dds, normalized = TRUE)</code>.</p></td>
</tr>
<tr>
<th>xs</th>
<td><p>Character, colname in colData that will be used as X-axes.</p></td>
</tr>
<tr>
<th>res</th>
<td><p><a href='https://rdrr.io/pkg/DESeq2/man/DESeqResults.html'>DESeq2::DESeqResults</a> object.</p></td>
</tr>
<tr>
<th>n</th>
<td><p>Integer number of genes to plot from the <code>res</code> object. It will
take the top N using padj values to order the table.</p></td>
</tr>
<tr>
<th>genes</th>
<td><p>Character of gene names matching rownames of count data.</p></td>
</tr>
<tr>
<th>group</th>
<td><p>Character, colname in colData to color points and add different
lines for each level.</p></td>
</tr>
<tr>
<th>batch</th>
<td><p>Character, colname in colData to shape points, normally used by
batch effect visualization.</p></td>
</tr>
<tr>
<th>metadata</th>
<td><p>Metadata in case dds is a matrix.</p></td>
</tr>
<tr>
<th>ann</th>
<td><p>Columns in rowData (if available) used to print gene names. First
element in the vector is the column name in rowData that matches the
row.names of the <code>dds</code> or <code>count</code> object. Second element in the vector
is the column name in rowData that it will be used as the title for each
gene or feature figure.</p></td>
</tr>
<tr>
<th>slot</th>
<td><p>Name of the slot to use to get count data.</p></td>
</tr>
<tr>
<th>log2</th>
<td><p>Whether to apply or not log2 transformation.</p></td>
</tr>
<tr>
<th>xsLab</th>
<td><p>Character, alternative label for x-axis (default: same as xs)</p></td>
</tr>
<tr>
<th>ysLab</th>
<td><p>Character, alternative label for y-axis..</p></td>
</tr>
<tr>
<th>color</th>
<td><p>Color to use to plot groups. It can be one color, or a palette
compatible with <code><a href='https://ggplot2.tidyverse.org/reference/scale_brewer.html'>ggplot2::scale_color_brewer()</a></code>.</p></td>
</tr>
<tr>
<th>groupLab</th>
<td><p>Character, alternative label for group (default: same as group).</p></td>
</tr>
<tr>
<th>batchLab</th>
<td><p>Character, alternative label for batch (default: same as batch).</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>ggplot showing the expresison of the genes</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/utils/data.html'>data</a></span>(<span class='no'>humanGender</span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>DESeq2</span>)
<span class='no'>idx</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>:<span class='fl'>10</span>, <span class='fl'>75</span>:<span class='fl'>85</span>)
<span class='no'>dse</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/DESeq2/man/DESeqDataSet.html'>DESeqDataSetFromMatrix</a></span>(<span class='fu'>assays</span>(<span class='no'>humanGender</span>)<span class='kw'>[[</span><span class='fl'>1</span>]][<span class='fl'>1</span>:<span class='fl'>1000</span>, <span class='no'>idx</span>],
<span class='fu'>colData</span>(<span class='no'>humanGender</span>)[<span class='no'>idx</span>,], <span class='kw'>design</span><span class='kw'>=</span>~<span class='no'>group</span>)
<span class='no'>dse</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/DESeq2/man/DESeq.html'>DESeq</a></span>(<span class='no'>dse</span>)</div><div class='output co'>#> <span class='message'>using pre-existing 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='output co'>#> <span class='message'>-- replacing outliers and refitting for 1 genes</span>
#> <span class='message'>-- DESeq argument 'minReplicatesForReplace' = 7 </span>
#> <span class='message'>-- original counts are preserved in counts(dds)</span></div><div class='output co'>#> <span class='message'>estimating dispersions</span></div><div class='output co'>#> <span class='message'>fitting model and testing</span></div><div class='input'><span class='fu'>degPlot</span>(<span class='no'>dse</span>, <span class='kw'>genes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>dse</span>)[<span class='fl'>1</span>:<span class='fl'>10</span>], <span class='kw'>xs</span> <span class='kw'>=</span> <span class='st'>"group"</span>)</div><div class='output co'>#> <span class='message'>No genes were mapped to rowData. check ann parameter values.</span></div><div class='output co'>#> <span class='message'>Using gene as id variables</span></div><div class='img'><img src='degPlot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>degPlot</span>(<span class='no'>dse</span>, <span class='kw'>genes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>dse</span>)[<span class='fl'>1</span>:<span class='fl'>10</span>], <span class='kw'>xs</span> <span class='kw'>=</span> <span class='st'>"group"</span>, <span class='kw'>color</span> <span class='kw'>=</span> <span class='st'>"orange"</span>)</div><div class='output co'>#> <span class='message'>No genes were mapped to rowData. check ann parameter values.</span></div><div class='output co'>#> <span class='message'>Using gene as id variables</span></div><div class='img'><img src='degPlot-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>degPlot</span>(<span class='no'>dse</span>, <span class='kw'>genes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>dse</span>)[<span class='fl'>1</span>:<span class='fl'>10</span>], <span class='kw'>xs</span> <span class='kw'>=</span> <span class='st'>"group"</span>, <span class='kw'>group</span> <span class='kw'>=</span> <span class='st'>"group"</span>,
<span class='kw'>color</span> <span class='kw'>=</span> <span class='st'>"Accent"</span>)</div><div class='output co'>#> <span class='message'>No genes were mapped to rowData. check ann parameter values.</span></div><div class='output co'>#> <span class='message'>Using gene as id variables</span></div><div class='img'><img src='degPlot-3.png' alt='' width='700' height='433' /></div></pre>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#examples">Examples</a></li>
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