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number of levels is &amp;gt; 3 or a set or orange/blue colors other wise." />
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    <h1>Make nice colors for metadata</h1>
    
    <div class="hidden name"><code>degColors.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>The function will take a metadata table and use Set2 palette when
number of levels is &gt; 3 or a set or orange/blue colors other wise.</p>
    </div>

    <pre class="usage"><span class='fu'>degColors</span>(<span class='no'>ann</span>, <span class='kw'>col_fun</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>con_values</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"grey80"</span>, <span class='st'>"black"</span>),
  <span class='kw'>cat_values</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"orange"</span>, <span class='st'>"steelblue"</span>), <span class='kw'>palette</span> <span class='kw'>=</span> <span class='st'>"Set2"</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>ann</th>
      <td><p>Data.frame with metadata information. Each column will be used to
generate a palette suitable for the values in there.</p></td>
    </tr>
    <tr>
      <th>col_fun</th>
      <td><p>Whether to return a function for continuous variables
(compatible with <code><a href='https://rdrr.io/pkg/ComplexHeatmap/man/HeatmapAnnotation.html'>ComplexHeatmap::HeatmapAnnotation()</a></code>) or
the colors themself (comparible with [pheatmap::pheatmap())]).</p>
<p>[pheatmap::pheatmap())]: R:pheatmap::pheatmap())</p></td>
    </tr>
    <tr>
      <th>con_values</th>
      <td><p>Color to be used for continuous variables.</p></td>
    </tr>
    <tr>
      <th>cat_values</th>
      <td><p>Color to be used for 2-levels categorical variables.</p></td>
    </tr>
    <tr>
      <th>palette</th>
      <td><p>Palette to use from <code>brewer.pal()</code> for
multi-levels categorical variables.</p></td>
    </tr>
    </table>


    <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='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>ComplexHeatmap</span>)</div><div class='output co'>#&gt; <span class='message'>Loading required package: grid</span></div><div class='output co'>#&gt; <span class='message'>========================================</span>
#&gt; <span class='message'>ComplexHeatmap version 2.1.0</span>
#&gt; <span class='message'>Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/</span>
#&gt; <span class='message'>Github page: https://github.com/jokergoo/ComplexHeatmap</span>
#&gt; <span class='message'>Documentation: http://jokergoo.github.io/ComplexHeatmap-reference</span>
#&gt; <span class='message'></span>
#&gt; <span class='message'>If you use it in published research, please cite:</span>
#&gt; <span class='message'>Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional </span>
#&gt; <span class='message'>  genomic data. Bioinformatics 2016.</span>
#&gt; <span class='message'>========================================</span></div><div class='input'><span class='no'>idx</span> <span class='kw'>&lt;-</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'>&lt;-</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'>10</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'>th</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/ComplexHeatmap/man/HeatmapAnnotation.html'>HeatmapAnnotation</a></span>(<span class='kw'>df</span> <span class='kw'>=</span> <span class='fu'>colData</span>(<span class='no'>dse</span>),
                       <span class='kw'>col</span> <span class='kw'>=</span> <span class='fu'>degColors</span>(<span class='fu'>colData</span>(<span class='no'>dse</span>), <span class='fl'>TRUE</span>))
<span class='fu'><a href='https://rdrr.io/pkg/ComplexHeatmap/man/Heatmap.html'>Heatmap</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log2</a></span>(<span class='fu'><a href='https://rdrr.io/pkg/DESeq2/man/counts.html'>counts</a></span>(<span class='no'>dse</span>)+<span class='fl'>0.5</span>), <span class='kw'>top_annotation</span> <span class='kw'>=</span> <span class='no'>th</span>)</div><div class='img'><img src='degColors-1.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='no'>custom</span> <span class='kw'>&lt;-</span> <span class='fu'>degColors</span>(<span class='fu'>colData</span>(<span class='no'>dse</span>), <span class='fl'>TRUE</span>,
          <span class='kw'>con_values</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"white"</span>, <span class='st'>"red"</span>),
          <span class='kw'>cat_values</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"white"</span>, <span class='st'>"black"</span>),
          <span class='kw'>palette</span> <span class='kw'>=</span> <span class='st'>"Set1"</span>)
<span class='no'>th</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/ComplexHeatmap/man/HeatmapAnnotation.html'>HeatmapAnnotation</a></span>(<span class='kw'>df</span> <span class='kw'>=</span> <span class='fu'>colData</span>(<span class='no'>dse</span>),
                        <span class='kw'>col</span> <span class='kw'>=</span> <span class='no'>custom</span>)
<span class='fu'><a href='https://rdrr.io/pkg/ComplexHeatmap/man/Heatmap.html'>Heatmap</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log2</a></span>(<span class='fu'><a href='https://rdrr.io/pkg/DESeq2/man/counts.html'>counts</a></span>(<span class='no'>dse</span>)+<span class='fl'>0.5</span>), <span class='kw'>top_annotation</span> <span class='kw'>=</span> <span class='no'>th</span>)</div><div class='img'><img src='degColors-2.png' alt='' width='700' height='433' /></div></pre>
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      <li><a href="#arguments">Arguments</a></li>
      <li><a href="#examples">Examples</a></li>
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