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<center><h1>Upset plot</h1></center>
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<center><p style="max-width: 600px; margin-top: 40px">An Upset plot is an alternative to the <a href="venn-diagram.html">Venn Diagram</a> used to deal with more than 3 sets. It is built in <code>R</code> thanks to the <code>upSetR</code> package.</p></center>
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<a class="btn btn-secondary btn-xl text-uppercase js-scroll-trigger" href='venn-diagram.html'>Venn diagram section</a>
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<h1 id="most-basic">Most basic</h1>
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<p><img src="upset-plot_files/figure-html/theCode-1.png" width="672" style="display: block; margin: auto;" /></p>
<p>To visualize the intersection between more than 3 sets, the best option is to use an UpSet plot.</p>
<p>Here is an example provided by the <code>UpsetR</code> package that displays information concerning the Banana genome.</p>
<p>The total size of each set is represented on the left barplot. Every possible intersection is represented by the bottom plot, and their occurence is shown on the top barplot.</p>
<p><u>Source</u>: the <a href="https://github.com/hms-dbmi/UpSetR">upSetR documentation</a></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Specific library</span>
<span class="kw">library</span>(UpSetR)
<span class="co"># Dataset</span>
input <-<span class="st"> </span><span class="kw">c</span>(
<span class="dt">M.acuminata =</span> <span class="dv">759</span>,
<span class="dt">P.dactylifera =</span> <span class="dv">769</span>,
<span class="dt">A.thaliana =</span> <span class="dv">1187</span>,
<span class="dt">O.sativa =</span> <span class="dv">1246</span>,
<span class="dt">S.bicolor =</span> <span class="dv">827</span>,
<span class="dt">B.distachyon =</span> <span class="dv">387</span>,
<span class="st">"P.dactylifera&M.acuminata"</span> =<span class="st"> </span><span class="dv">467</span>,
<span class="st">"O.sativa&M.acuminata"</span> =<span class="st"> </span><span class="dv">29</span>,
<span class="st">"A.thaliana&O.sativa"</span> =<span class="st"> </span><span class="dv">6</span>,
<span class="st">"S.bicolor&A.thaliana"</span> =<span class="st"> </span><span class="dv">9</span>,
<span class="st">"O.sativa&P.dactylifera"</span> =<span class="st"> </span><span class="dv">32</span>,
<span class="st">"S.bicolor&P.dactylifera"</span> =<span class="st"> </span><span class="dv">49</span>,
<span class="st">"S.bicolor&M.acuminata"</span> =<span class="st"> </span><span class="dv">49</span>,
<span class="st">"B.distachyon&O.sativa"</span> =<span class="st"> </span><span class="dv">547</span>,
<span class="st">"S.bicolor&O.sativa"</span> =<span class="st"> </span><span class="dv">1151</span>,
<span class="st">"B.distachyon&A.thaliana"</span> =<span class="st"> </span><span class="dv">10</span>,
<span class="st">"B.distachyon&M.acuminata"</span> =<span class="st"> </span><span class="dv">9</span>,
<span class="st">"B.distachyon&S.bicolor"</span> =<span class="st"> </span><span class="dv">402</span>,
<span class="st">"M.acuminata&A.thaliana"</span> =<span class="st"> </span><span class="dv">155</span>,
<span class="st">"A.thaliana&P.dactylifera"</span> =<span class="st"> </span><span class="dv">105</span>,
<span class="st">"B.distachyon&P.dactylifera"</span> =<span class="st"> </span><span class="dv">25</span>,
<span class="st">"S.bicolor&O.sativa&P.dactylifera"</span> =<span class="st"> </span><span class="dv">42</span>,
<span class="st">"B.distachyon&O.sativa&P.dactylifera"</span> =<span class="st"> </span><span class="dv">12</span>,
<span class="st">"S.bicolor&O.sativa&B.distachyon"</span> =<span class="st"> </span><span class="dv">2809</span>,
<span class="st">"B.distachyon&O.sativa&A.thaliana"</span> =<span class="st"> </span><span class="dv">18</span>,
<span class="st">"S.bicolor&O.sativa&A.thaliana"</span> =<span class="st"> </span><span class="dv">40</span>,
<span class="st">"S.bicolor&B.distachyon&A.thaliana"</span> =<span class="st"> </span><span class="dv">14</span>,
<span class="st">"O.sativa&B.distachyon&M.acuminata"</span> =<span class="st"> </span><span class="dv">28</span>,
<span class="st">"S.bicolor&B.distachyon&M.acuminata"</span> =<span class="st"> </span><span class="dv">13</span>,
<span class="st">"O.sativa&M.acuminata&P.dactylifera"</span> =<span class="st"> </span><span class="dv">35</span>,
<span class="st">"M.acuminata&S.bicolor&A.thaliana"</span> =<span class="st"> </span><span class="dv">21</span>,
<span class="st">"B.distachyon&M.acuminata&A.thaliana"</span> =<span class="st"> </span><span class="dv">7</span>,
<span class="st">"O.sativa&M.acuminata&A.thaliana"</span> =<span class="st"> </span><span class="dv">13</span>,
<span class="st">"M.acuminata&P.dactylifera&A.thaliana"</span> =<span class="st"> </span><span class="dv">206</span>,
<span class="st">"P.dactylifera&A.thaliana&S.bicolor"</span> =<span class="st"> </span><span class="dv">4</span>,
<span class="st">"O.sativa&A.thaliana&P.dactylifera"</span> =<span class="st"> </span><span class="dv">6</span>,
<span class="st">"S.bicolor&O.sativa&M.acuminata"</span> =<span class="st"> </span><span class="dv">64</span>,
<span class="st">"S.bicolor&M.acuminata&P.dactylifera"</span> =<span class="st"> </span><span class="dv">19</span>,
<span class="st">"B.distachyon&A.thaliana&P.dactylifera"</span> =<span class="st"> </span><span class="dv">3</span>,
<span class="st">"B.distachyon&M.acuminata&P.dactylifera"</span> =<span class="st"> </span><span class="dv">12</span>,
<span class="st">"B.distachyon&S.bicolor&P.dactylifera"</span> =<span class="st"> </span><span class="dv">23</span>,
<span class="st">"M.acuminata&B.distachyon&S.bicolor&A.thaliana"</span> =<span class="st"> </span><span class="dv">54</span>,
<span class="st">"P.dactylifera&S.bicolor&O.sativa&M.acuminata"</span> =<span class="st"> </span><span class="dv">62</span>,
<span class="st">"B.distachyon&O.sativa&M.acuminata&P.dactylifera"</span> =<span class="st"> </span><span class="dv">18</span>,
<span class="st">"S.bicolor&B.distachyon&O.sativa&A.thaliana"</span> =<span class="st"> </span><span class="dv">206</span>,
<span class="st">"B.distachyon&M.acuminata&O.sativa&A.thaliana"</span> =<span class="st"> </span><span class="dv">29</span>,
<span class="st">"O.sativa&M.acuminata&A.thaliana&S.bicolor"</span> =<span class="st"> </span><span class="dv">71</span>,
<span class="st">"M.acuminata&O.sativa&P.dactylifera&A.thaliana"</span> =<span class="st"> </span><span class="dv">28</span>,
<span class="st">"B.distachyon&M.acuminata&O.sativa&A.thaliana"</span> =<span class="st"> </span><span class="dv">7</span>,
<span class="st">"B.distachyon&S.bicolor&P.dactylifera&A.thaliana"</span> =<span class="st"> </span><span class="dv">11</span>,
<span class="st">"B.distachyon&O.sativa&P.dactylifera&A.thaliana"</span> =<span class="st"> </span><span class="dv">5</span>,
<span class="st">"A.thaliana&P.dactylifera&S.bicolor&O.sativa"</span> =<span class="st"> </span><span class="dv">21</span>,
<span class="st">"M.acuminata&S.bicolor&P.dactylifera&A.thaliana"</span> =<span class="st"> </span><span class="dv">23</span>,
<span class="st">"M.acuminata&B.distachyon&S.bicolor&P.dactylifera"</span> =<span class="st"> </span><span class="dv">24</span>,
<span class="st">"M.acuminata&O.sativa&S.bicolor&B.distachyon"</span> =<span class="st"> </span><span class="dv">368</span>,
<span class="st">"P.dactylifera&B.distachyon&S.bicolor&O.sativa"</span> =<span class="st"> </span><span class="dv">190</span>,
<span class="st">"P.dactylifera&B.distachyon&S.bicolor&O.sativa&A.thaliana"</span> =<span class="st"> </span><span class="dv">258</span>,
<span class="st">"P.dactylifera&M.acuminata&S.bicolor&B.distachyon&O.sativa"</span> =<span class="st"> </span><span class="dv">685</span>,
<span class="st">"M.acuminata&S.bicolor&B.distachyon&O.sativa&A.thaliana"</span> =<span class="st"> </span><span class="dv">1458</span>,
<span class="st">"S.bicolor&M.acuminata&P.dactylifera&O.sativa&A.thaliana"</span> =<span class="st"> </span><span class="dv">149</span>,
<span class="st">"B.distachyon&M.acuminata&P.dactylifera&O.sativa&A.thaliana"</span> =<span class="st"> </span><span class="dv">80</span>,
<span class="st">"M.acuminata&S.bicolor&B.distachyon&P.dactylifera&A.thaliana"</span> =<span class="st"> </span><span class="dv">113</span>,
<span class="st">"M.acuminata&S.bicolor&B.distachyon&P.dactylifera&O.sativa&A.thaliana"</span> =<span class="st"> </span><span class="dv">7674</span>
)
<span class="co"># Plot</span>
<span class="kw">upset</span>(<span class="kw">fromExpression</span>(input),
<span class="dt">nintersects =</span> <span class="dv">40</span>,
<span class="dt">nsets =</span> <span class="dv">6</span>,
<span class="dt">order.by =</span> <span class="st">"freq"</span>,
<span class="dt">decreasing =</span> T,
<span class="dt">mb.ratio =</span> <span class="kw">c</span>(<span class="fl">0.6</span>, <span class="fl">0.4</span>),
<span class="dt">number.angles =</span> <span class="dv">0</span>,
<span class="dt">text.scale =</span> <span class="fl">1.1</span>,
<span class="dt">point.size =</span> <span class="fl">2.8</span>,
<span class="dt">line.size =</span> <span class="dv">1</span>
)</code></pre></div>
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