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<center><h1>ggplot2 heatmap</h1></center>
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<center><p style="max-width: 600px; margin-top: 40px">This document provides several examples of <a href="heatmap.html">heatmaps</a> built with <code>R</code> and <a href="ggplot2.html">ggplot2</a>. It describes the main customization you can apply, with explanation and reproducible code.<br><u>Note:</u> The native <a href="215-the-heatmap-function.html">heatmap() function</a> provides more options for data normalization and clustering. Consider it as a valuable option.</p></center>
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<h1 id="most-basic-heatmap-with-ggplot2">Most basic heatmap with <code>ggplot2</code></h1>
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<p>This is the most basic heatmap you can build with <code>R</code> and <code>ggplot2</code>, using the <code>geom_tile()</code> function.</p>
<p>Input data must be a long format where each row provides an observation. At least 3 variables are needed per observation:</p>
<ul>
<li><code>x</code>: position on the X axis</li>
<li><code>y</code>: position on the Y axis</li>
<li><code>fill</code>: the numeric value that will be translated in a color</li>
</ul>
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<p><img src="79-levelplot-with-ggplot2_files/figure-html/thecode-1.png" width="100%" /></p>
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<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Library</span>
<span class="kw">library</span>(ggplot2)
<span class="co"># Dummy data</span>
x <-<span class="st"> </span>LETTERS[<span class="dv">1</span><span class="op">:</span><span class="dv">20</span>]
y <-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"var"</span>, <span class="kw">seq</span>(<span class="dv">1</span>,<span class="dv">20</span>))
data <-<span class="st"> </span><span class="kw">expand.grid</span>(<span class="dt">X=</span>x, <span class="dt">Y=</span>y)
data<span class="op">$</span>Z <-<span class="st"> </span><span class="kw">runif</span>(<span class="dv">400</span>, <span class="dv">0</span>, <span class="dv">5</span>)
<span class="co"># Heatmap </span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(X, Y, <span class="dt">fill=</span> Z)) <span class="op">+</span><span class="st"> </span>
<span class="st"> </span><span class="kw">geom_tile</span>()</code></pre></div>
<h1 id="control-color-palette">Control color palette</h1>
<hr />
<p><img src="79-levelplot-with-ggplot2_files/figure-html/thecode2-1.png" width="33%" /><img src="79-levelplot-with-ggplot2_files/figure-html/thecode2-2.png" width="33%" /><img src="79-levelplot-with-ggplot2_files/figure-html/thecode2-3.png" width="33%" /></p>
<p>Color palette can be changed like in any <a href="ggplot2.html">ggplot2</a> chart. Above are 3 examples using different methods:</p>
<ul>
<li><code>scale_fill_gradient()</code> to provide extreme colors of the palette</li>
<li><code>scale_fill_distiller)</code> to provide a <a href="38-rcolorbrewers-palettes.html">ColorBrewer</a> palette</li>
<li><code>scale_fill_viridis()</code> to use Viridis. Do not forget <code>discrete=FALSE</code> for a continuous variable.</li>
</ul>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Library</span>
<span class="kw">library</span>(ggplot2)
<span class="kw">library</span>(hrbrthemes)
<span class="co"># Dummy data</span>
x <-<span class="st"> </span>LETTERS[<span class="dv">1</span><span class="op">:</span><span class="dv">20</span>]
y <-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"var"</span>, <span class="kw">seq</span>(<span class="dv">1</span>,<span class="dv">20</span>))
data <-<span class="st"> </span><span class="kw">expand.grid</span>(<span class="dt">X=</span>x, <span class="dt">Y=</span>y)
data<span class="op">$</span>Z <-<span class="st"> </span><span class="kw">runif</span>(<span class="dv">400</span>, <span class="dv">0</span>, <span class="dv">5</span>)
<span class="co"># Give extreme colors:</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(X, Y, <span class="dt">fill=</span> Z)) <span class="op">+</span><span class="st"> </span>
<span class="st"> </span><span class="kw">geom_tile</span>() <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_fill_gradient</span>(<span class="dt">low=</span><span class="st">"white"</span>, <span class="dt">high=</span><span class="st">"blue"</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">theme_ipsum</span>()
<span class="co"># Color Brewer palette</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(X, Y, <span class="dt">fill=</span> Z)) <span class="op">+</span><span class="st"> </span>
<span class="st"> </span><span class="kw">geom_tile</span>() <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_fill_distiller</span>(<span class="dt">palette =</span> <span class="st">"RdPu"</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">theme_ipsum</span>()
<span class="co"># Color Brewer palette</span>
<span class="kw">library</span>(viridis)
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(X, Y, <span class="dt">fill=</span> Z)) <span class="op">+</span><span class="st"> </span>
<span class="st"> </span><span class="kw">geom_tile</span>() <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_fill_viridis</span>(<span class="dt">discrete=</span><span class="ot">FALSE</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">theme_ipsum</span>()</code></pre></div>
<h1 id="from-wide-input-format">From wide input format</h1>
<hr />
<div class="row">
<div class="col-md-6 col-sm-12 align-self-center">
<p>It is a common issue to have a wide matrix as input, as for the <code>volcano</code> dataset. In this case, you need to tidy it with the <code>gather()</code> function of the <code>tidyr</code> package to visualize it with <a href="ggplot2.html">ggplot</a>.</p>
</div>
<div class="col-md-6 col-sm-12">
<p><img src="79-levelplot-with-ggplot2_files/figure-html/thecode3-1.png" width="100%" /></p>
</div>
</div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Library</span>
<span class="kw">library</span>(ggplot2)
<span class="kw">library</span>(tidyr)
<span class="kw">library</span>(tibble)
<span class="kw">library</span>(hrbrthemes)
<span class="kw">library</span>(dplyr)
<span class="co"># Volcano dataset</span>
<span class="co">#volcano</span>
<span class="co"># Heatmap </span>
volcano <span class="op">%>%</span>
<span class="st"> </span>
<span class="st"> </span><span class="co"># Data wrangling</span>
<span class="st"> </span><span class="kw">as_tibble</span>() <span class="op">%>%</span>
<span class="st"> </span><span class="kw">rowid_to_column</span>(<span class="dt">var=</span><span class="st">"X"</span>) <span class="op">%>%</span>
<span class="st"> </span><span class="kw">gather</span>(<span class="dt">key=</span><span class="st">"Y"</span>, <span class="dt">value=</span><span class="st">"Z"</span>, <span class="op">-</span><span class="dv">1</span>) <span class="op">%>%</span>
<span class="st"> </span>
<span class="st"> </span><span class="co"># Change Y to numeric</span>
<span class="st"> </span><span class="kw">mutate</span>(<span class="dt">Y=</span><span class="kw">as.numeric</span>(<span class="kw">gsub</span>(<span class="st">"V"</span>,<span class="st">""</span>,Y))) <span class="op">%>%</span>
<span class="st"> </span><span class="co"># Viz</span>
<span class="st"> </span><span class="kw">ggplot</span>(<span class="kw">aes</span>(X, Y, <span class="dt">fill=</span> Z)) <span class="op">+</span><span class="st"> </span>
<span class="st"> </span><span class="kw">geom_tile</span>() <span class="op">+</span>
<span class="st"> </span><span class="kw">theme_ipsum</span>() <span class="op">+</span>
<span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position=</span><span class="st">"none"</span>)</code></pre></div>
<h1 id="turn-it-interactive-with-plotly">Turn it interactive with <code>plotly</code></h1>
<hr />
<div class="row">
<div class="col-md-5 col-sm-12 align-self-center">
<p>One of the nice feature of <a href="ggplot2.html">ggplot2</a> is that charts can be turned interactive in seconds thanks to <code>plotly</code>. You just need to wrap your chart in an object and call it in the <code>ggplotly()</code> function.</p>
<p>Often, it is a good practice to custom the text available in the tooltip.</p>
<p><u>Note: </u>try to hover cells to see the tooltip, select an area to zoom in.</p>
</div>
<div class="col-md-7 col-sm-12">
<center>
<iframe src="HtmlWidget/ggplotlyHeatmap.html" height="700" width="700" style="border:none;">
</iframe>
</center>
</div>
</div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Library</span>
<span class="kw">library</span>(ggplot2)
<span class="kw">library</span>(hrbrthemes)
<span class="kw">library</span>(plotly)
<span class="co"># Dummy data</span>
x <-<span class="st"> </span>LETTERS[<span class="dv">1</span><span class="op">:</span><span class="dv">20</span>]
y <-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"var"</span>, <span class="kw">seq</span>(<span class="dv">1</span>,<span class="dv">20</span>))
data <-<span class="st"> </span><span class="kw">expand.grid</span>(<span class="dt">X=</span>x, <span class="dt">Y=</span>y)
data<span class="op">$</span>Z <-<span class="st"> </span><span class="kw">runif</span>(<span class="dv">400</span>, <span class="dv">0</span>, <span class="dv">5</span>)
<span class="co"># new column: text for tooltip:</span>
data <-<span class="st"> </span>data <span class="op">%>%</span>
<span class="st"> </span><span class="kw">mutate</span>(<span class="dt">text =</span> <span class="kw">paste0</span>(<span class="st">"x: "</span>, x, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>, <span class="st">"y: "</span>, y, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>, <span class="st">"Value: "</span>,<span class="kw">round</span>(Z,<span class="dv">2</span>), <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>, <span class="st">"What else?"</span>))
<span class="co"># classic ggplot, with text in aes</span>
p <-<span class="st"> </span><span class="kw">ggplot</span>(data, <span class="kw">aes</span>(X, Y, <span class="dt">fill=</span> Z, <span class="dt">text=</span>text)) <span class="op">+</span><span class="st"> </span>
<span class="st"> </span><span class="kw">geom_tile</span>() <span class="op">+</span>
<span class="st"> </span><span class="kw">theme_ipsum</span>()
<span class="kw">ggplotly</span>(p, <span class="dt">tooltip=</span><span class="st">"text"</span>)
<span class="co"># save the widget</span>
<span class="co"># library(htmlwidgets)</span>
<span class="co"># saveWidget(pp, file=paste0( getwd(), "/HtmlWidget/ggplotlyHeatmap.html"))</span></code></pre></div>
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