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<center><h1>Circular chart customization for the circlize R package</h1></center>
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<center><p style="max-width: 600px; margin-top: 40px">This post follows the previous <a href="224-basic-circular-plot.html">introduction</a> to the <code>circlize</code> package. It shows how to apply basic customizations to a circular chart: how to change track width, background color, start angle and more.</p></center>
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<h1 id="most-basic-circular-chart">Most basic circular chart</h1>
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<p>Let’s remind how to build a basic circular chart with the <code>circlize</code> package.</p>
<p>This is extensively described in <a href="224-basic-circular-plot.html">chart #224</a>.</p>
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<p><img src="225-circular-plot-custom-a-track_files/figure-html/thecode-1.png" width="100%" /></p>
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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)</a></code></pre></div>
<h1 id="customization">Customization</h1>
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<p>Customization can happen at 3 different levels:</p>
<ul>
<li>initialization: use the usual <code>par()</code> function and the specific <code>circos.par()</code> functions for general stuff.</li>
<li>in <code>circos.axis()</code> to customize axis</li>
<li>in circos.trackPoints()` to customize the chart shapes.</li>
</ul>
<p>Note that most of the parameters are consistent with base R. Have a look to the <a href="scatterplot.html">scatterplot</a> section of the gallery for more customization.</p>
</div>
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<p><img src="225-circular-plot-custom-a-track_files/figure-html/thecode2-1.png" width="100%" /></p>
</div>
</div>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="co"># Upload library</span></a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">library</span>(circlize)</a>
<a class="sourceLine" id="cb2-3" data-line-number="3"></a>
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co"># Create data</span></a>
<a class="sourceLine" id="cb2-5" data-line-number="5">data =<span class="st"> </span><span class="kw">data.frame</span>(</a>
<a class="sourceLine" id="cb2-6" 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="cb2-7" data-line-number="7"> <span class="dt">x =</span> <span class="kw">rnorm</span>(<span class="dv">1000</span>),</a>
<a class="sourceLine" id="cb2-8" data-line-number="8"> <span class="dt">y =</span> <span class="kw">runif</span>(<span class="dv">1000</span>)</a>
<a class="sourceLine" id="cb2-9" data-line-number="9"> )</a>
<a class="sourceLine" id="cb2-10" data-line-number="10"></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co"># General Customization:</span></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="kw">par</span>(</a>
<a class="sourceLine" id="cb2-13" data-line-number="13"> <span class="dt">mar =</span> <span class="kw">c</span>(<span class="dv">1</span>, <span class="dv">1</span>, <span class="dv">1</span>, <span class="dv">1</span>), <span class="co"># Margin around chart</span></a>
<a class="sourceLine" id="cb2-14" data-line-number="14"> <span class="dt">bg =</span> <span class="kw">rgb</span>(<span class="fl">0.4</span>,<span class="fl">0.1</span>,<span class="fl">0.7</span>,<span class="fl">0.05</span>) <span class="co"># background color</span></a>
<a class="sourceLine" id="cb2-15" data-line-number="15">) </a>
<a class="sourceLine" id="cb2-16" data-line-number="16"><span class="kw">circos.par</span>(<span class="st">"track.height"</span> =<span class="st"> </span><span class="fl">0.6</span>) <span class="co"># track hight, 0.6 = 60% of total height</span></a>
<a class="sourceLine" id="cb2-17" data-line-number="17"></a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># Step1: Initialise the chart giving factor and x-axis.</span></a>
<a class="sourceLine" id="cb2-19" data-line-number="19"><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">$</span>x )</a>
<a class="sourceLine" id="cb2-20" data-line-number="20"></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># Step2: Build regions. </span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="kw">circos.trackPlotRegion</span>(<span class="dt">factors =</span> data<span class="op">$</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="cb2-23" data-line-number="23"> <span class="kw">circos.axis</span>(</a>
<a class="sourceLine" id="cb2-24" data-line-number="24"> <span class="dt">h=</span><span class="st">"top"</span>, <span class="co"># x axis on the inner or outer part of the track?</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"> <span class="dt">labels=</span><span class="ot">TRUE</span>, <span class="co"># show the labels of the axis?</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"> <span class="dt">major.tick=</span><span class="ot">TRUE</span>, <span class="co"># show ticks?</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"> <span class="dt">labels.cex=</span><span class="fl">0.5</span>, <span class="co"># labels size (higher=bigger)</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"> <span class="dt">labels.font=</span><span class="dv">1</span>, <span class="co"># labels font (1, 2, 3 , 4)</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"> <span class="dt">direction=</span><span class="st">"outside"</span>, <span class="co"># ticks point to the outside or inside of the circle ?</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"> <span class="dt">minor.ticks=</span><span class="dv">4</span>, <span class="co"># Number of minor (=small) ticks</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"> <span class="dt">major.tick.percentage=</span><span class="fl">0.1</span>, <span class="co"># The size of the ticks in percentage of the track height</span></a>
<a class="sourceLine" id="cb2-32" data-line-number="32"> <span class="dt">lwd=</span><span class="dv">2</span> <span class="co"># thickness of ticks and x axis.</span></a>
<a class="sourceLine" id="cb2-33" data-line-number="33"> )</a>
<a class="sourceLine" id="cb2-34" data-line-number="34"> })</a>
<a class="sourceLine" id="cb2-35" data-line-number="35"></a>
<a class="sourceLine" id="cb2-36" data-line-number="36"><span class="co"># Step 3: Add points</span></a>
<a class="sourceLine" id="cb2-37" data-line-number="37"><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">"#69b3a2"</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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