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<center><h1>Introduction to the circlize package</h1></center>
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<center><p style="max-width: 600px; margin-top: 40px">This post is an introductioni to the <code>circlize</code> package: the ultimate way to build <a href="chord-diagram.html">circular charts</a> with R. It shows how to initialize a circular section and fill it with a <a href="scatterplot.html">scatterplot</a>.</p></center>
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<p>In R, circular plots are made using the <code>circlize</code> package. Circular plots are composed by several regions (8 here), each representing a level of a factor. Three steps are required to build a circular plot:</p>
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<li><p><em>Step 1</em>: Initialize the chart with <code>circos.initialize()</code>. Provide the factor vector, and the numeric values to use for the X axis. The circle will be split in as many zone as the number of levels present in your factor. Each region will be as long as the coresponding x axis.</p></li>
<li><p><em>Step2</em>: Build the regions with <code>circos.trackPlotRegion()</code>. You have to specify the factors once again, and tell what to use for the Y axis if needed.</p></li>
<li><p><em>Step3</em>: Add a chart in each region. Here <code>circos.trackPoints()</code> is used to build a scatterplot. See <a href="226-plot-types-for-circular-plot.html">chart #226</a> for other chart types.</p></li>
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="co"># Upload library</span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw">library</span>(circlize)</a>
<a class="sourceLine" id="cb1-3" data-line-number="3"> </a>
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co"># Create data</span></a>
<a class="sourceLine" id="cb1-5" data-line-number="5">data =<span class="st"> </span><span class="kw">data.frame</span>(</a>
<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="dt">factor =</span> <span class="kw">sample</span>(letters[<span class="dv">1</span><span class="op">:</span><span class="dv">8</span>], <span class="dv">1000</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>),</a>
<a class="sourceLine" id="cb1-7" data-line-number="7"> <span class="dt">x =</span> <span class="kw">rnorm</span>(<span class="dv">1000</span>), </a>
<a class="sourceLine" id="cb1-8" data-line-number="8"> <span class="dt">y =</span> <span class="kw">runif</span>(<span class="dv">1000</span>)</a>
<a class="sourceLine" id="cb1-9" data-line-number="9"> )</a>
<a class="sourceLine" id="cb1-10" data-line-number="10"> </a>
<a class="sourceLine" id="cb1-11" data-line-number="11"><span class="co"># Step1: Initialise the chart giving factor and x-axis.</span></a>
<a class="sourceLine" id="cb1-12" data-line-number="12"><span class="kw">circos.initialize</span>( <span class="dt">factors=</span>data<span class="op">$</span>factor, <span class="dt">x=</span>data<span class="op">$</span>x )</a>
<a class="sourceLine" id="cb1-13" data-line-number="13"> </a>
<a class="sourceLine" id="cb1-14" data-line-number="14"><span class="co"># Step 2: Build the regions. </span></a>
<a class="sourceLine" id="cb1-15" data-line-number="15"><span class="kw">circos.trackPlotRegion</span>(<span class="dt">factors =</span> data<span class="op">$</span>factor, <span class="dt">y =</span> data<span class="op">$</span>y, <span class="dt">panel.fun =</span> <span class="cf">function</span>(x, y) {</a>
<a class="sourceLine" id="cb1-16" data-line-number="16"> <span class="kw">circos.axis</span>()</a>
<a class="sourceLine" id="cb1-17" data-line-number="17"> })</a>
<a class="sourceLine" id="cb1-18" data-line-number="18"> </a>
<a class="sourceLine" id="cb1-19" data-line-number="19"><span class="co"># Step 3: Add points</span></a>
<a class="sourceLine" id="cb1-20" data-line-number="20"><span class="kw">circos.trackPoints</span>(data<span class="op">$</span>factor, data<span class="op">$</span>x, data<span class="op">$</span>y, <span class="dt">col =</span> <span class="st">"blue"</span>, <span class="dt">pch =</span> <span class="dv">16</span>, <span class="dt">cex =</span> <span class="fl">0.5</span>) </a></code></pre></div>
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