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<center><h1>2d density plot with ggplot2</h1></center>
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<center><p style="max-width: 600px; margin-top: 40px">This post introduces the concept of 2d density chart and explains how to build it with R and ggplot2. 2d histograms, hexbin charts, 2d distributions and others are considered.</p></center>
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<a class="btn btn-secondary btn-xl text-uppercase js-scroll-trigger" href='2d-density-chart.html'>2d density section</a>
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<h1 id="the-issue-with-geom_point">The issue with <code>geom_point()</code></h1>
<hr />
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<p>A <a href="2d-density-chart.html">2d density plot</a> is useful to study the relationship between 2 numeric variables if you have a huge number of points.</p>
<p>To avoid overlapping (as in the scatterplot beside), it divides the plot area in a multitude of small fragment and represents the number of points in this fragment.</p>
<p>There are several types of 2d density plots. Each has its proper <a href="ggplot2.html">ggplot2</a> function. This post describes all of them.</p>
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<div class="col-md-6 col-sm-12">
<p><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode-1.png" width="100%" /></p>
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</div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Library</span>
<span class="kw">library</span>(tidyverse)
<span class="co"># Data</span>
a <-<span class="st"> </span><span class="kw">data.frame</span>( <span class="dt">x=</span><span class="kw">rnorm</span>(<span class="dv">20000</span>, <span class="dv">10</span>, <span class="fl">1.9</span>), <span class="dt">y=</span><span class="kw">rnorm</span>(<span class="dv">20000</span>, <span class="dv">10</span>, <span class="fl">1.2</span>) )
b <-<span class="st"> </span><span class="kw">data.frame</span>( <span class="dt">x=</span><span class="kw">rnorm</span>(<span class="dv">20000</span>, <span class="fl">14.5</span>, <span class="fl">1.9</span>), <span class="dt">y=</span><span class="kw">rnorm</span>(<span class="dv">20000</span>, <span class="fl">14.5</span>, <span class="fl">1.9</span>) )
c <-<span class="st"> </span><span class="kw">data.frame</span>( <span class="dt">x=</span><span class="kw">rnorm</span>(<span class="dv">20000</span>, <span class="fl">9.5</span>, <span class="fl">1.9</span>), <span class="dt">y=</span><span class="kw">rnorm</span>(<span class="dv">20000</span>, <span class="fl">15.5</span>, <span class="fl">1.9</span>) )
data <-<span class="st"> </span><span class="kw">rbind</span>(a,b,c)
<span class="co"># Basic scatterplot</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">geom_point</span>()</code></pre></div>
<p><br><br></p>
<h1 id="hist">2d Histogram with <code>geom_bin2d()</code></h1>
<hr />
<p><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode2-1.png" width="40%" /><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode2-2.png" width="40%" /></p>
<div class="row">
<div class="col-md-6 col-sm-12 align-self-center">
<p>For 2d histogram, the plot area is divided in a multitude of squares. (It is a 2d version of the classic <a href="histogram.html">histogram</a>). It is called using the <code>geom_bin_2d()</code> function. This function offers a <code>bins</code> argument that controls the number of bins you want to display.</p>
<p><u>Note</u>: If you’re not convinced about the importance of the <code>bins</code> option, read <a href="https://www.data-to-viz.com/caveat/bin_size.html">this</a>.</p>
</div>
<div class="col-md-6 col-sm-12">
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># 2d histogram with default option</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">geom_bin2d</span>() <span class="op">+</span>
<span class="st"> </span><span class="kw">theme_bw</span>()
<span class="co"># Bin size control + color palette</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">geom_bin2d</span>(<span class="dt">bins =</span> <span class="dv">70</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_fill_continuous</span>(<span class="dt">type =</span> <span class="st">"viridis"</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">theme_bw</span>()</code></pre></div>
</div>
</div>
<p><br><br></p>
<h1 id="hex">Hexbin chart with <code>geom_hex()</code></h1>
<hr />
<p><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode3-1.png" width="40%" /><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode3-2.png" width="40%" /></p>
<div class="row">
<div class="col-md-6 col-sm-12 align-self-center">
<p>Another alternative is to divide the plot area in a multitude of hexagons: it is thus called a hexbin chart, and is made using the <code>geom_hex()</code> function.</p>
<p>This function provides the <code>bins</code> argument as well, to control the number of division per axis.</p>
</div>
<div class="col-md-6 col-sm-12">
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Hexbin chart with default option</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">geom_hex</span>() <span class="op">+</span>
<span class="st"> </span><span class="kw">theme_bw</span>()
<span class="co"># Bin size control + color palette</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">geom_hex</span>(<span class="dt">bins =</span> <span class="dv">70</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_fill_continuous</span>(<span class="dt">type =</span> <span class="st">"viridis"</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">theme_bw</span>()</code></pre></div>
</div>
</div>
<p><br><br></p>
<h1 id="distr">2d distribution with <code>geom_density_2d</code> or <code>stat_density_2d</code></h1>
<hr />
<p><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode4-1.png" width="50%" /><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode4-2.png" width="50%" /><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode4-3.png" width="50%" /><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode4-4.png" width="50%" /></p>
<p>As you can plot a <a href="density.html">density chart</a> instead of a <a href="histogram.html">histogram</a>, it is possible to compute a 2d density and represent it. Several possibilities are offered by <code>ggplot2</code>: you can show the contour of the distribution, or the area, or use the <code>raster</code> function:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Show the contour only</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">geom_density_2d</span>()
<span class="co"># Show the area only</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">stat_density_2d</span>(<span class="kw">aes</span>(<span class="dt">fill =</span> ..level..), <span class="dt">geom =</span> <span class="st">"polygon"</span>)
<span class="co"># Area + contour</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">stat_density_2d</span>(<span class="kw">aes</span>(<span class="dt">fill =</span> ..level..), <span class="dt">geom =</span> <span class="st">"polygon"</span>, <span class="dt">colour=</span><span class="st">"white"</span>)
<span class="co"># Using raster</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">stat_density_2d</span>(<span class="kw">aes</span>(<span class="dt">fill =</span> ..density..), <span class="dt">geom =</span> <span class="st">"raster"</span>, <span class="dt">contour =</span> <span class="ot">FALSE</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_x_continuous</span>(<span class="dt">expand =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">0</span>)) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_y_continuous</span>(<span class="dt">expand =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">0</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>
<p><br><br></p>
<h1 id="customize-the-color-palette">Customize the color palette</h1>
<hr />
<p><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode5-1.png" width="33%" /><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode5-2.png" width="33%" /><img src="2d-density-plot-with-ggplot2_files/figure-html/thecode5-3.png" width="33%" /></p>
<p>Whatever you use a 2d histogram, a hexbin chart or a 2d distribution, you can and should custom the colour of your chart. Here is a suggestion using the <code>scale_fill_distiller()</code> function. You can see other methods in the <a href="ggplot2.html">ggplot2 section</a> of the gallery.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Call the palette with a number</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">stat_density_2d</span>(<span class="kw">aes</span>(<span class="dt">fill =</span> ..density..), <span class="dt">geom =</span> <span class="st">"raster"</span>, <span class="dt">contour =</span> <span class="ot">FALSE</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_fill_distiller</span>(<span class="dt">palette=</span><span class="dv">4</span>, <span class="dt">direction=</span><span class="op">-</span><span class="dv">1</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_x_continuous</span>(<span class="dt">expand =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">0</span>)) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_y_continuous</span>(<span class="dt">expand =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">0</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>
)
<span class="co"># The direction argument allows to reverse the palette</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">stat_density_2d</span>(<span class="kw">aes</span>(<span class="dt">fill =</span> ..density..), <span class="dt">geom =</span> <span class="st">"raster"</span>, <span class="dt">contour =</span> <span class="ot">FALSE</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_fill_distiller</span>(<span class="dt">palette=</span><span class="dv">4</span>, <span class="dt">direction=</span><span class="dv">1</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_x_continuous</span>(<span class="dt">expand =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">0</span>)) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_y_continuous</span>(<span class="dt">expand =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">0</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>
)
<span class="co"># You can also call the palette using a name.</span>
<span class="kw">ggplot</span>(data, <span class="kw">aes</span>(<span class="dt">x=</span>x, <span class="dt">y=</span>y) ) <span class="op">+</span>
<span class="st"> </span><span class="kw">stat_density_2d</span>(<span class="kw">aes</span>(<span class="dt">fill =</span> ..density..), <span class="dt">geom =</span> <span class="st">"raster"</span>, <span class="dt">contour =</span> <span class="ot">FALSE</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_fill_distiller</span>(<span class="dt">palette=</span> <span class="st">"Spectral"</span>, <span class="dt">direction=</span><span class="dv">1</span>) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_x_continuous</span>(<span class="dt">expand =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">0</span>)) <span class="op">+</span>
<span class="st"> </span><span class="kw">scale_y_continuous</span>(<span class="dt">expand =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">0</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>
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<p>This document is a work by <a href="https://www.yan-holtz.com">Yan Holtz</a>. Any feedback is highly encouraged. You can fill an issue on <a href="https://github.com/holtzy/D3-graph-gallery/issues">Github</a>, drop me a message on <a href="https://twitter.com/R_Graph_Gallery">Twitter</a>, or send an email pasting <a href="">yan.holtz.data</a> with <a href="">gmail.com</a>.</p>
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