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<center><h1>Advanced chord diagram with R and circlize</h1></center>
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<center><p style="max-width: 600px; margin-top: 40px"><a href="chord-diagram.html">Chord diagram</a> is an efficient way to display flows between entities. This post shows how to build it from an edge list or from an adjacency matrix, using the <code>circlize</code> package.</p></center>
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<a class="btn btn-secondary btn-xl text-uppercase js-scroll-trigger" href='chord-diagram.html'>Chord section</a>
<a class="btn btn-secondary btn-xl text-uppercase js-scroll-trigger" href='https://www.data-to-viz.com/graph/chord.html'>Data to Viz</a>
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<h1 id="chord-diagram-from-adjacency-matrix">Chord diagram from adjacency matrix</h1>
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<p>The <code>chordDiagram()</code> function of the <code>circlize</code> package makes it a breeze to build chord diagrams from adjacency matrix in R.</p>
<p>The adjacency matrix displays all origins in rows, and all destinations in columns. Each cell is filled with a numeric value specifying the flow strength.</p>
<p><u>Note</u>: visit the <a href="chord-diagram.html">chord section</a> of the gallery or the circlize <a href="https://cran.r-project.org/web/packages/circlize/vignettes/circlize.pdf">vignette</a> for more chord examples.</p>
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<p><img src="123-circular-plot-circlize-package-2_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"># Create an adjacency matrix: </span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co"># a list of connections between 20 origin nodes, and 5 destination nodes:</span></a>
<a class="sourceLine" id="cb1-3" data-line-number="3">numbers <-<span class="st"> </span><span class="kw">sample</span>(<span class="kw">c</span>(<span class="dv">1</span><span class="op">:</span><span class="dv">1000</span>), <span class="dv">100</span>, <span class="dt">replace =</span> T)</a>
<a class="sourceLine" id="cb1-4" data-line-number="4">data <-<span class="st"> </span><span class="kw">matrix</span>( numbers, <span class="dt">ncol=</span><span class="dv">5</span>)</a>
<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="kw">rownames</span>(data) <-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"orig-"</span>, <span class="kw">seq</span>(<span class="dv">1</span>,<span class="dv">20</span>))</a>
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="kw">colnames</span>(data) <-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"dest-"</span>, <span class="kw">seq</span>(<span class="dv">1</span>,<span class="dv">5</span>))</a>
<a class="sourceLine" id="cb1-7" data-line-number="7"></a>
<a class="sourceLine" id="cb1-8" data-line-number="8"><span class="co"># Load the circlize library</span></a>
<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="kw">library</span>(circlize)</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"># Make the circular plot</span></a>
<a class="sourceLine" id="cb1-12" data-line-number="12"><span class="kw">chordDiagram</span>(data, <span class="dt">transparency =</span> <span class="fl">0.5</span>)</a></code></pre></div>
<h1 id="chord-diagram-from-edge-list">Chord diagram from edge list</h1>
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<p>Another common format to store flow information iis the edge list. Basically, all connections are stored one by one in a 2 columns file, listing the origin and destination of each.</p>
<p>Since the <code>chordDiagram()</code> function expects an adjacency matrix as input, it is required to use the <code>table()</code> function for reformating, as described below:</p>
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<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"># Create an edge list: a list of connections between 10 origin nodes, and 10 destination nodes:</span></a>
<a class="sourceLine" id="cb2-2" data-line-number="2">origin <-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"orig "</span>, <span class="kw">sample</span>(<span class="kw">c</span>(<span class="dv">1</span><span class="op">:</span><span class="dv">10</span>), <span class="dv">20</span>, <span class="dt">replace =</span> T))</a>
<a class="sourceLine" id="cb2-3" data-line-number="3">destination <-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"dest "</span>, <span class="kw">sample</span>(<span class="kw">c</span>(<span class="dv">1</span><span class="op">:</span><span class="dv">10</span>), <span class="dv">20</span>, <span class="dt">replace =</span> T))</a>
<a class="sourceLine" id="cb2-4" data-line-number="4">data <-<span class="st"> </span><span class="kw">data.frame</span>(origin, destination)</a>
<a class="sourceLine" id="cb2-5" data-line-number="5"></a>
<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="co"># Transform input data in a adjacency matrix</span></a>
<a class="sourceLine" id="cb2-7" data-line-number="7">adjacencyData <-<span class="st"> </span><span class="kw">with</span>(data, <span class="kw">table</span>(origin, destination))</a>
<a class="sourceLine" id="cb2-8" data-line-number="8"> </a>
<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="co"># Charge the circlize library</span></a>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="kw">library</span>(circlize)</a>
<a class="sourceLine" id="cb2-11" data-line-number="11"> </a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># Make the circular plot</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="kw">chordDiagram</span>(adjacencyData, <span class="dt">transparency =</span> <span class="fl">0.5</span>)</a></code></pre></div>
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