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<!DOCTYPE html>
<html lang="en"><head>
<script src="index_files/libs/clipboard/clipboard.min.js"></script>
<script src="index_files/libs/quarto-html/tabby.min.js"></script>
<script src="index_files/libs/quarto-html/popper.min.js"></script>
<script src="index_files/libs/quarto-html/tippy.umd.min.js"></script>
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<link href="index_files/libs/quarto-html/quarto-syntax-highlighting-dark.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
<meta name="generator" content="quarto-1.3.353">
<meta name="author" content="Jeremy Selva ">
<title>Chapter 2: Data Visualisation</title>
<meta name="apple-mobile-web-app-capable" content="yes">
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<div class="quarto-title-author-name">
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</div>
</div>
</div>
</section>
<section id="introduction" class="slide level2">
<h2>Introduction</h2>
<p>This chapter shows how to visualise data using <code>ggplot2</code>. Ensure these libraries are available.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="co"># Needed in the book</span></span>
<span id="cb1-2"><a href="#cb1-2"></a><span class="fu">library</span>(tidyverse)</span>
<span id="cb1-3"><a href="#cb1-3"></a><span class="fu">library</span>(palmerpenguins)</span>
<span id="cb1-4"><a href="#cb1-4"></a><span class="fu">library</span>(ggthemes)</span>
<span id="cb1-5"><a href="#cb1-5"></a></span>
<span id="cb1-6"><a href="#cb1-6"></a><span class="co"># For the extra slides</span></span>
<span id="cb1-7"><a href="#cb1-7"></a><span class="fu">library</span>(scales)</span>
<span id="cb1-8"><a href="#cb1-8"></a><span class="fu">library</span>(glue)</span>
<span id="cb1-9"><a href="#cb1-9"></a><span class="fu">library</span>(ggfittext)</span>
<span id="cb1-10"><a href="#cb1-10"></a><span class="fu">library</span>(ggtext)</span>
<span id="cb1-11"><a href="#cb1-11"></a><span class="fu">library</span>(downloadthis)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
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</div>
</section>
<section id="penguins-data" class="slide level2">
<h2><code>penguins</code> data</h2>
<p>The <code>penguins</code> data has 344 penguins observations with 8 columns.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a><span class="fu">print</span>(penguins, <span class="at">width =</span> <span class="cn">Inf</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 344 × 8
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
<fct> <fct> <dbl> <dbl> <int> <int>
1 Adelie Torgersen 39.1 18.7 181 3750
2 Adelie Torgersen 39.5 17.4 186 3800
3 Adelie Torgersen 40.3 18 195 3250
4 Adelie Torgersen NA NA NA NA
5 Adelie Torgersen 36.7 19.3 193 3450
6 Adelie Torgersen 39.3 20.6 190 3650
7 Adelie Torgersen 38.9 17.8 181 3625
8 Adelie Torgersen 39.2 19.6 195 4675
9 Adelie Torgersen 34.1 18.1 193 3475
10 Adelie Torgersen 42 20.2 190 4250
sex year
<fct> <int>
1 male 2007
2 female 2007
3 female 2007
4 <NA> 2007
5 female 2007
6 male 2007
7 female 2007
8 male 2007
9 <NA> 2007
10 <NA> 2007
# ℹ 334 more rows</code></pre>
</div>
</div>
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</div>
</section>
<section id="penguins-data-1" class="slide level2">
<h2><code>penguins</code> data</h2>
<p>Among the variables in penguins are:</p>
<ol type="1">
<li><p><code>species</code>: a penguin’s species (Adelie, Chinstrap, or Gentoo).</p></li>
<li><p><code>flipper_length_mm</code>: length of a penguin’s flipper, in millimeters.</p></li>
<li><p><code>body_mass_g</code>: body mass of a penguin, in grams.</p></li>
</ol>
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</div>
</section>
<section id="penguins-data-2" class="slide level2">
<h2><code>penguins</code> data</h2>
<p>We can take a closer look using <code>dplyr::glimpse()</code></p>
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a>dplyr<span class="sc">::</span><span class="fu">glimpse</span>(penguins)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>Rows: 344
Columns: 8
$ species <fct> Adelie, Adelie, Adelie, Adelie, Adelie, Adelie, Adel…
$ island <fct> Torgersen, Torgersen, Torgersen, Torgersen, Torgerse…
$ bill_length_mm <dbl> 39.1, 39.5, 40.3, NA, 36.7, 39.3, 38.9, 39.2, 34.1, …
$ bill_depth_mm <dbl> 18.7, 17.4, 18.0, NA, 19.3, 20.6, 17.8, 19.6, 18.1, …
$ flipper_length_mm <int> 181, 186, 195, NA, 193, 190, 181, 195, 193, 190, 186…
$ body_mass_g <int> 3750, 3800, 3250, NA, 3450, 3650, 3625, 4675, 3475, …
$ sex <fct> male, female, female, NA, female, male, female, male…
$ year <int> 2007, 2007, 2007, 2007, 2007, 2007, 2007, 2007, 2007…</code></pre>
</div>
</div>
<p>We try to find a relationship between flipper lengths and body masses for each penguins species.</p>
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</div>
</section>
<section id="creating-a-ggplot" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>The first argument <code>data</code> is to tell <code>ggplot</code> which the dataset to use in the graph. It gives an empty graph at first.</p>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb6-2"><a href="#cb6-2"></a> <span class="at">data =</span> penguins</span>
<span id="cb6-3"><a href="#cb6-3"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column">
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/unnamed-chunk-4-1.png" alt="An empty graph." width="960"></p>
</div>
</div>
</div>
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</div>
</section>
<section id="creating-a-ggplot-1" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>The next argument <code>mapping</code> tells <code>ggplot</code> what variables in <code>penguins</code> holds the x and y axis. The <code>mapping</code> argument must be an output of the <code>ggplot2::aes</code> function.</p>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb7" data-code-line-numbers="|3-6"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb7-2"><a href="#cb7-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb7-3"><a href="#cb7-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb7-4"><a href="#cb7-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb7-5"><a href="#cb7-5"></a> <span class="at">y =</span> body_mass_g</span>
<span id="cb7-6"><a href="#cb7-6"></a> )</span>
<span id="cb7-7"><a href="#cb7-7"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column">
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/unnamed-chunk-5-1.png" alt="A graph with only x and y axis labels." width="960"></p>
</div>
</div>
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</div>
</section>
<section id="creating-a-ggplot-2" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>We can see that flipper lengths and body mass are displayed in the x and y axis. However, we cannot see the penguin data in the plot.</p>
<div class="cell columns column-output-location">
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<div class="sourceCode cell-code" id="cb8" data-code-line-numbers="3-6"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb8-2"><a href="#cb8-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb8-3"><a href="#cb8-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb8-4"><a href="#cb8-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb8-5"><a href="#cb8-5"></a> <span class="at">y =</span> body_mass_g</span>
<span id="cb8-6"><a href="#cb8-6"></a> )</span>
<span id="cb8-7"><a href="#cb8-7"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p><img data-src="index_files/figure-revealjs/unnamed-chunk-6-1.png" alt="A graph with only x and y axis labels." width="960"></p>
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</div>
</section>
<section id="creating-a-ggplot-3" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>We need to specify using <code>geom_</code> what the data should be represented as a</p>
<ul>
<li>bar using <code>geom_bar()</code></li>
<li>line using <code>geom_line()</code></li>
<li>boxplot using <code>geom_boxplot()</code></li>
<li>scatterplots using <code>geom_point()</code></li>
</ul>
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</div>
</section>
<section id="creating-a-ggplot-4" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>Adding <code>geom_point()</code> gives us the points in the plot. We can see that penguins with longer flippers are generally larger in their body mass.</p>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb9" data-code-line-numbers="|8"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb9-2"><a href="#cb9-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb9-3"><a href="#cb9-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb9-4"><a href="#cb9-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb9-5"><a href="#cb9-5"></a> <span class="at">y =</span> body_mass_g</span>
<span id="cb9-6"><a href="#cb9-6"></a> )</span>
<span id="cb9-7"><a href="#cb9-7"></a>) <span class="sc">+</span> </span>
<span id="cb9-8"><a href="#cb9-8"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing missing values (`geom_point()`).</code></pre>
</div>
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/unnamed-chunk-7-1.png" alt="A scatterplot of penguin's body mass in grams vs flipper length in mm." width="960"></p>
</div>
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</div>
</section>
<section id="creating-a-ggplot-5" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>The warning indicates that two of the penguins have missing body mass and/or flipper length values.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1"></a>penguins <span class="sc">|></span> </span>
<span id="cb11-2"><a href="#cb11-2"></a> dplyr<span class="sc">::</span><span class="fu">filter</span>(</span>
<span id="cb11-3"><a href="#cb11-3"></a> <span class="fu">is.na</span>(flipper_length_mm) <span class="sc">|</span> <span class="fu">is.na</span>(body_mass_g)</span>
<span id="cb11-4"><a href="#cb11-4"></a> ) <span class="sc">|></span></span>
<span id="cb11-5"><a href="#cb11-5"></a> <span class="fu">print</span>(<span class="at">width =</span> <span class="cn">Inf</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 2 × 8
species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
<fct> <fct> <dbl> <dbl> <int> <int>
1 Adelie Torgersen NA NA NA NA
2 Gentoo Biscoe NA NA NA NA
sex year
<fct> <int>
1 <NA> 2007
2 <NA> 2009</code></pre>
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</div>
</section>
<section id="creating-a-ggplot-6" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>In general, we can see that penguins with longer flippers are generally larger in their body mass.</p>
<p>Does this applies for all species (Adelie, Chinstrap and Gentoo) ?</p>
<p>We can do this by representing species with different coloured points.</p>
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</div>
</section>
<section id="creating-a-ggplot-7" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>To do this, we modify the <code>aes</code> function by adding <code>color = species</code>.</p>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb13" data-code-line-numbers="|6"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb13-2"><a href="#cb13-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb13-3"><a href="#cb13-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb13-4"><a href="#cb13-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb13-5"><a href="#cb13-5"></a> <span class="at">y =</span> body_mass_g,</span>
<span id="cb13-6"><a href="#cb13-6"></a> <span class="at">color =</span> species</span>
<span id="cb13-7"><a href="#cb13-7"></a> )</span>
<span id="cb13-8"><a href="#cb13-8"></a>) <span class="sc">+</span> </span>
<span id="cb13-9"><a href="#cb13-9"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column">
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing missing values (`geom_point()`).</code></pre>
</div>
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/unnamed-chunk-9-1.png" alt="A scatterplot of penguin's body mass in grams vs flipper length in mm with colours." width="960"></p>
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</div>
</section>
<section id="creating-a-ggplot-8" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>Adding <code>color = species</code> allows <code>ggplot</code> to assign a unique colour for each species and provides a legend.</p>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb15" data-code-line-numbers="6"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb15-2"><a href="#cb15-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb15-3"><a href="#cb15-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb15-4"><a href="#cb15-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb15-5"><a href="#cb15-5"></a> <span class="at">y =</span> body_mass_g,</span>
<span id="cb15-6"><a href="#cb15-6"></a> <span class="at">color =</span> species</span>
<span id="cb15-7"><a href="#cb15-7"></a> )</span>
<span id="cb15-8"><a href="#cb15-8"></a>) <span class="sc">+</span> </span>
<span id="cb15-9"><a href="#cb15-9"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column">
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing missing values (`geom_point()`).</code></pre>
</div>
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/unnamed-chunk-10-1.png" alt="A scatterplot of penguin's body mass in grams vs flipper length in mm with colours." width="960"></p>
</div>
</div>
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</div>
</section>
<section id="creating-a-ggplot-9" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>We now wish to add a smooth curve for each species. this is done by adding <code>geom_smooth(method = "lm")</code></p>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb17" data-code-line-numbers="|10"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb17-2"><a href="#cb17-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb17-3"><a href="#cb17-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb17-4"><a href="#cb17-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb17-5"><a href="#cb17-5"></a> <span class="at">y =</span> body_mass_g,</span>
<span id="cb17-6"><a href="#cb17-6"></a> <span class="at">color =</span> species</span>
<span id="cb17-7"><a href="#cb17-7"></a> )</span>
<span id="cb17-8"><a href="#cb17-8"></a>) <span class="sc">+</span> </span>
<span id="cb17-9"><a href="#cb17-9"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>() <span class="sc">+</span></span>
<span id="cb17-10"><a href="#cb17-10"></a>ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(<span class="at">method =</span> <span class="st">"lm"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column">
<div class="cell-output cell-output-stderr">
<pre><code>`geom_smooth()` using formula = 'y ~ x'</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing non-finite values (`stat_smooth()`).</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing missing values (`geom_point()`).</code></pre>
</div>
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/unnamed-chunk-11-1.png" alt="A scatterplot of penguin's body mass in grams vs flipper length in mm with smooth curves for each species." width="960"></p>
</div>
</div>
</div>
<div class="footer">
<p>https://jauntyjjs.github.io/r4ds-bookclub-cohort9-chapter02 <a href="https://jauntyjjs.github.io/r4ds-bookclub-cohort9-chapter02/"><svg aria-hidden="true" role="img" viewbox="0 0 640 512" style="height:1em;width:1.25em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M579.8 267.7c56.5-56.5 56.5-148 0-204.5c-50-50-128.8-56.5-186.3-15.4l-1.6 1.1c-14.4 10.3-17.7 30.3-7.4 44.6s30.3 17.7 44.6 7.4l1.6-1.1c32.1-22.9 76-19.3 103.8 8.6c31.5 31.5 31.5 82.5 0 114L422.3 334.8c-31.5 31.5-82.5 31.5-114 0c-27.9-27.9-31.5-71.8-8.6-103.8l1.1-1.6c10.3-14.4 6.9-34.4-7.4-44.6s-34.4-6.9-44.6 7.4l-1.1 1.6C206.5 251.2 213 330 263 380c56.5 56.5 148 56.5 204.5 0L579.8 267.7zM60.2 244.3c-56.5 56.5-56.5 148 0 204.5c50 50 128.8 56.5 186.3 15.4l1.6-1.1c14.4-10.3 17.7-30.3 7.4-44.6s-30.3-17.7-44.6-7.4l-1.6 1.1c-32.1 22.9-76 19.3-103.8-8.6C74 372 74 321 105.5 289.5L217.7 177.2c31.5-31.5 82.5-31.5 114 0c27.9 27.9 31.5 71.8 8.6 103.9l-1.1 1.6c-10.3 14.4-6.9 34.4 7.4 44.6s34.4 6.9 44.6-7.4l1.1-1.6C433.5 260.8 427 182 377 132c-56.5-56.5-148-56.5-204.5 0L60.2 244.3z"></path></svg></a> <a href="https://github.com/JauntyJJS/r4ds-bookclub-cohort9-chapter02"><svg aria-hidden="true" role="img" viewbox="0 0 496 512" style="height:1em;width:0.97em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg></a></p>
</div>
</section>
<section id="creating-a-ggplot-10" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>Instead of a line for all species, how do we add only one smooth curve to describe the relationship for all species ?</p>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb21"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb21-2"><a href="#cb21-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb21-3"><a href="#cb21-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb21-4"><a href="#cb21-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb21-5"><a href="#cb21-5"></a> <span class="at">y =</span> body_mass_g,</span>
<span id="cb21-6"><a href="#cb21-6"></a> <span class="at">color =</span> species</span>
<span id="cb21-7"><a href="#cb21-7"></a> )</span>
<span id="cb21-8"><a href="#cb21-8"></a>) <span class="sc">+</span> </span>
<span id="cb21-9"><a href="#cb21-9"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>() <span class="sc">+</span></span>
<span id="cb21-10"><a href="#cb21-10"></a>ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(<span class="at">method =</span> <span class="st">"lm"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column">
<div class="cell-output cell-output-stderr">
<pre><code>`geom_smooth()` using formula = 'y ~ x'</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing non-finite values (`stat_smooth()`).</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing missing values (`geom_point()`).</code></pre>
</div>
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/unnamed-chunk-12-1.png" alt="A scatterplot of penguin's body mass in grams vs flipper length in mm with smooth curves for each species." width="960"></p>
</div>
</div>
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</div>
</section>
<section id="creating-a-ggplot-11" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>We need to agree that the following are equivalent.</p>
<div class="columns">
<div class="column" style="width:50%;">
<div class="cell">
<div class="sourceCode cell-code" id="cb25" data-code-line-numbers="|1,3-6"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb25-2"><a href="#cb25-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb25-3"><a href="#cb25-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb25-4"><a href="#cb25-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb25-5"><a href="#cb25-5"></a> <span class="at">y =</span> body_mass_g,</span>
<span id="cb25-6"><a href="#cb25-6"></a> <span class="at">color =</span> species)</span>
<span id="cb25-7"><a href="#cb25-7"></a>) <span class="sc">+</span> </span>
<span id="cb25-8"><a href="#cb25-8"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>() <span class="sc">+</span></span>
<span id="cb25-9"><a href="#cb25-9"></a>ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(<span class="at">method =</span> <span class="st">"lm"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div><div class="column" style="width:50%;">
<div class="cell">
<div class="sourceCode cell-code" id="cb26" data-code-line-numbers="|2,4-7,9,11-14"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb26-1"><a href="#cb26-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>() <span class="sc">+</span> </span>
<span id="cb26-2"><a href="#cb26-2"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>(</span>
<span id="cb26-3"><a href="#cb26-3"></a> <span class="at">data =</span> penguins,</span>
<span id="cb26-4"><a href="#cb26-4"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb26-5"><a href="#cb26-5"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb26-6"><a href="#cb26-6"></a> <span class="at">y =</span> body_mass_g,</span>
<span id="cb26-7"><a href="#cb26-7"></a> <span class="at">color =</span> species)</span>
<span id="cb26-8"><a href="#cb26-8"></a>) <span class="sc">+</span></span>
<span id="cb26-9"><a href="#cb26-9"></a>ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(</span>
<span id="cb26-10"><a href="#cb26-10"></a> <span class="at">data =</span> penguins,</span>
<span id="cb26-11"><a href="#cb26-11"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb26-12"><a href="#cb26-12"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb26-13"><a href="#cb26-13"></a> <span class="at">y =</span> body_mass_g,</span>
<span id="cb26-14"><a href="#cb26-14"></a> <span class="at">color =</span> species),</span>
<span id="cb26-15"><a href="#cb26-15"></a> <span class="at">method =</span> <span class="st">"lm"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
</section>
<section id="creating-a-ggplot-12" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>Because we want to draw a smooth curve along all species, we need to remove the <code>color = species</code> in the <code>mapping</code> argument of <code>geom_smooth</code>.</p>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb27" data-code-line-numbers="|9,11-13"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb27-1"><a href="#cb27-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>() <span class="sc">+</span> </span>
<span id="cb27-2"><a href="#cb27-2"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>(</span>
<span id="cb27-3"><a href="#cb27-3"></a> <span class="at">data =</span> penguins,</span>
<span id="cb27-4"><a href="#cb27-4"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb27-5"><a href="#cb27-5"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb27-6"><a href="#cb27-6"></a> <span class="at">y =</span> body_mass_g,</span>
<span id="cb27-7"><a href="#cb27-7"></a> <span class="at">color =</span> species)</span>
<span id="cb27-8"><a href="#cb27-8"></a>) <span class="sc">+</span></span>
<span id="cb27-9"><a href="#cb27-9"></a>ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(</span>
<span id="cb27-10"><a href="#cb27-10"></a> <span class="at">data =</span> penguins,</span>
<span id="cb27-11"><a href="#cb27-11"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb27-12"><a href="#cb27-12"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb27-13"><a href="#cb27-13"></a> <span class="at">y =</span> body_mass_g),</span>
<span id="cb27-14"><a href="#cb27-14"></a> <span class="at">method =</span> <span class="st">"lm"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column">
<div class="cell-output cell-output-stderr">
<pre><code>`geom_smooth()` using formula = 'y ~ x'</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing non-finite values (`stat_smooth()`).</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing missing values (`geom_point()`).</code></pre>
</div>
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/unnamed-chunk-15-1.png" alt="A scatterplot of penguin's body mass in grams vs flipper length in mm with smooth curves for each species." width="960"></p>
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</div>
</section>
<section id="creating-a-ggplot-13" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>We put what mapping arguments that are common in <code>geom_point</code> and <code>geom_smooth</code> back to <code>ggplot</code>.</p>
<div class="columns">
<div class="column" style="width:50%;">
<div class="cell">
<div class="sourceCode cell-code" id="cb31" data-code-line-numbers="|2,5-6,9,11-13"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb31-1"><a href="#cb31-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>() <span class="sc">+</span> </span>
<span id="cb31-2"><a href="#cb31-2"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>(</span>
<span id="cb31-3"><a href="#cb31-3"></a> <span class="at">data =</span> penguins,</span>
<span id="cb31-4"><a href="#cb31-4"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb31-5"><a href="#cb31-5"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb31-6"><a href="#cb31-6"></a> <span class="at">y =</span> body_mass_g,</span>
<span id="cb31-7"><a href="#cb31-7"></a> <span class="at">color =</span> species)</span>
<span id="cb31-8"><a href="#cb31-8"></a>) <span class="sc">+</span></span>
<span id="cb31-9"><a href="#cb31-9"></a>ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(</span>
<span id="cb31-10"><a href="#cb31-10"></a> <span class="at">data =</span> penguins,</span>
<span id="cb31-11"><a href="#cb31-11"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb31-12"><a href="#cb31-12"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb31-13"><a href="#cb31-13"></a> <span class="at">y =</span> body_mass_g),</span>
<span id="cb31-14"><a href="#cb31-14"></a> <span class="at">method =</span> <span class="st">"lm"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div><div class="column" style="width:50%;">
<div class="cell">
<div class="sourceCode cell-code" id="cb32" data-code-line-numbers="|3-6"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb32-1"><a href="#cb32-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb32-2"><a href="#cb32-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb32-3"><a href="#cb32-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb32-4"><a href="#cb32-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb32-5"><a href="#cb32-5"></a> <span class="at">y =</span> body_mass_g</span>
<span id="cb32-6"><a href="#cb32-6"></a> )</span>
<span id="cb32-7"><a href="#cb32-7"></a>) <span class="sc">+</span> </span>
<span id="cb32-8"><a href="#cb32-8"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>(</span>
<span id="cb32-9"><a href="#cb32-9"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb32-10"><a href="#cb32-10"></a> <span class="at">color =</span> species)</span>
<span id="cb32-11"><a href="#cb32-11"></a>) <span class="sc">+</span></span>
<span id="cb32-12"><a href="#cb32-12"></a>ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(</span>
<span id="cb32-13"><a href="#cb32-13"></a> <span class="at">method =</span> <span class="st">"lm"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
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</div>
</section>
<section id="creating-a-ggplot-14" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>Here is the simplified code.</p>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb33"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb33-1"><a href="#cb33-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb33-2"><a href="#cb33-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb33-3"><a href="#cb33-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb33-4"><a href="#cb33-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb33-5"><a href="#cb33-5"></a> <span class="at">y =</span> body_mass_g</span>
<span id="cb33-6"><a href="#cb33-6"></a> )</span>
<span id="cb33-7"><a href="#cb33-7"></a>) <span class="sc">+</span> </span>
<span id="cb33-8"><a href="#cb33-8"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>(</span>
<span id="cb33-9"><a href="#cb33-9"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb33-10"><a href="#cb33-10"></a> <span class="at">color =</span> species)</span>
<span id="cb33-11"><a href="#cb33-11"></a>) <span class="sc">+</span></span>
<span id="cb33-12"><a href="#cb33-12"></a>ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(</span>
<span id="cb33-13"><a href="#cb33-13"></a> <span class="at">method =</span> <span class="st">"lm"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<div class="cell-output cell-output-stderr">
<pre><code>`geom_smooth()` using formula = 'y ~ x'</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing non-finite values (`stat_smooth()`).</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing missing values (`geom_point()`).</code></pre>
</div>
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/unnamed-chunk-18-1.png" alt="A scatterplot of penguin's body mass in grams vs flipper length in mm with a smooth curve." width="960"></p>
</div>
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</div>
</section>
<section id="creating-a-ggplot-15" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>Besides colour, we can create a different shape for each species.</p>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb37" data-code-line-numbers="|11"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb37-1"><a href="#cb37-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb37-2"><a href="#cb37-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb37-3"><a href="#cb37-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb37-4"><a href="#cb37-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb37-5"><a href="#cb37-5"></a> <span class="at">y =</span> body_mass_g</span>
<span id="cb37-6"><a href="#cb37-6"></a> )</span>
<span id="cb37-7"><a href="#cb37-7"></a>) <span class="sc">+</span> </span>
<span id="cb37-8"><a href="#cb37-8"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>(</span>
<span id="cb37-9"><a href="#cb37-9"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb37-10"><a href="#cb37-10"></a> <span class="at">color =</span> species,</span>
<span id="cb37-11"><a href="#cb37-11"></a> <span class="at">shape =</span> species)</span>
<span id="cb37-12"><a href="#cb37-12"></a>) <span class="sc">+</span></span>
<span id="cb37-13"><a href="#cb37-13"></a>ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(</span>
<span id="cb37-14"><a href="#cb37-14"></a> <span class="at">method =</span> <span class="st">"lm"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column">
<div class="cell-output cell-output-stderr">
<pre><code>`geom_smooth()` using formula = 'y ~ x'</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing non-finite values (`stat_smooth()`).</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: Removed 2 rows containing missing values (`geom_point()`).</code></pre>
</div>
<div class="cell-output-display">
<p><img data-src="index_files/figure-revealjs/unnamed-chunk-19-1.png" alt="A scatterplot of penguin's body mass in grams vs flipper length in mm with a smooth curve. Different species are indicated with different colour and shape." width="960"></p>
</div>
</div>
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</section>
<section id="creating-a-ggplot-16" class="slide level2">
<h2>Creating a <code>ggplot</code></h2>
<p>Next, we use <code>labs</code> to label the plot.</p>
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb41" data-code-line-numbers="|15-22"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb41-1"><a href="#cb41-1"></a>ggplot2<span class="sc">::</span><span class="fu">ggplot</span>(</span>
<span id="cb41-2"><a href="#cb41-2"></a> <span class="at">data =</span> penguins,</span>
<span id="cb41-3"><a href="#cb41-3"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb41-4"><a href="#cb41-4"></a> <span class="at">x =</span> flipper_length_mm, </span>
<span id="cb41-5"><a href="#cb41-5"></a> <span class="at">y =</span> body_mass_g</span>
<span id="cb41-6"><a href="#cb41-6"></a> )</span>
<span id="cb41-7"><a href="#cb41-7"></a>) <span class="sc">+</span> </span>
<span id="cb41-8"><a href="#cb41-8"></a>ggplot2<span class="sc">::</span><span class="fu">geom_point</span>(</span>
<span id="cb41-9"><a href="#cb41-9"></a> <span class="at">mapping =</span> ggplot2<span class="sc">::</span><span class="fu">aes</span>(</span>
<span id="cb41-10"><a href="#cb41-10"></a> <span class="at">color =</span> species,</span>
<span id="cb41-11"><a href="#cb41-11"></a> <span class="at">shape =</span> species)</span>
<span id="cb41-12"><a href="#cb41-12"></a>) <span class="sc">+</span></span>
<span id="cb41-13"><a href="#cb41-13"></a>ggplot2<span class="sc">::</span><span class="fu">geom_smooth</span>(</span>
<span id="cb41-14"><a href="#cb41-14"></a> <span class="at">method =</span> <span class="st">"lm"</span>) <span class="sc">+</span></span>
<span id="cb41-15"><a href="#cb41-15"></a>ggplot2<span class="sc">::</span><span class="fu">labs</span>(</span>
<span id="cb41-16"><a href="#cb41-16"></a> <span class="at">title =</span> <span class="st">"Body mass and flipper length"</span>,</span>
<span id="cb41-17"><a href="#cb41-17"></a> <span class="at">subtitle =</span> <span class="st">"Dimensions for Adelie, Chinstrap, and Gentoo Penguins"</span>,</span>
<span id="cb41-18"><a href="#cb41-18"></a> <span class="at">x =</span> <span class="st">"Flipper length (mm)"</span>, </span>
<span id="cb41-19"><a href="#cb41-19"></a> <span class="at">y =</span> <span class="st">"Body mass (g)"</span>,</span>
<span id="cb41-20"><a href="#cb41-20"></a> <span class="at">color =</span> <span class="st">"Species"</span>, </span>
<span id="cb41-21"><a href="#cb41-21"></a> <span class="at">shape =</span> <span class="st">"Species"</span></span>
<span id="cb41-22"><a href="#cb41-22"></a> ) </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<div class="cell-output cell-output-stderr">
<pre><code>`geom_smooth()` using formula = 'y ~ x'</code></pre>