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<div id="module-1-exercise-results" class="section level1 unnumbered">
<h1>Module 1 Exercise Results</h1>
<p>Load packages and data, subset needed columns:</p>
<div class="sourceCode" id="cb42"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb42-1"><a href="module-1-exercise-results.html#cb42-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(MASS)</span>
<span id="cb42-2"><a href="module-1-exercise-results.html#cb42-2" aria-hidden="true" tabindex="-1"></a><span class="fu">data</span>(crabs)</span></code></pre></div>
<p>Learn more about the data:</p>
<div class="sourceCode" id="cb43"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb43-1"><a href="module-1-exercise-results.html#cb43-1" aria-hidden="true" tabindex="-1"></a>?crabs</span>
<span id="cb43-2"><a href="module-1-exercise-results.html#cb43-2" aria-hidden="true" tabindex="-1"></a><span class="fu">head</span>(crabs)</span></code></pre></div>
<pre><code>## sp sex index FL RW CL CW BD
## 1 B M 1 8.1 6.7 16.1 19.0 7.0
## 2 B M 2 8.8 7.7 18.1 20.8 7.4
## 3 B M 3 9.2 7.8 19.0 22.4 7.7
## 4 B M 4 9.6 7.9 20.1 23.1 8.2
## 5 B M 5 9.8 8.0 20.3 23.0 8.2
## 6 B M 6 10.8 9.0 23.0 26.5 9.8</code></pre>
<p>Subset needed columns:</p>
<div class="sourceCode" id="cb45"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb45-1"><a href="module-1-exercise-results.html#cb45-1" aria-hidden="true" tabindex="-1"></a>crabs_meas <span class="ot"><-</span> crabs[,<span class="fu">c</span>(<span class="st">"FL"</span>,<span class="st">"RW"</span>,<span class="st">"CL"</span>,<span class="st">"CW"</span>,<span class="st">"BD"</span>)]</span></code></pre></div>
<p>Perform hierarchical clustering:</p>
<div class="sourceCode" id="cb46"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb46-1"><a href="module-1-exercise-results.html#cb46-1" aria-hidden="true" tabindex="-1"></a>c_dist <span class="ot"><-</span> <span class="fu">dist</span>(crabs_meas)</span>
<span id="cb46-2"><a href="module-1-exercise-results.html#cb46-2" aria-hidden="true" tabindex="-1"></a>c_hclust <span class="ot"><-</span> <span class="fu">hclust</span>(c_dist)</span>
<span id="cb46-3"><a href="module-1-exercise-results.html#cb46-3" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(c_hclust)</span></code></pre></div>
<p><img src="bookdown-demo_files/figure-html/unnamed-chunk-21-1.png" width="672" /></p>
<p>Colour-code samples based on cluster assignment. Assume there are two clusters.</p>
<div class="sourceCode" id="cb47"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb47-1"><a href="module-1-exercise-results.html#cb47-1" aria-hidden="true" tabindex="-1"></a>c_clusters <span class="ot">=</span> <span class="fu">cutree</span>(c_hclust,<span class="at">k =</span> <span class="dv">2</span>)</span></code></pre></div>
<p>Now create a pairs plot, but colour-code by:
1. by gene-expression based clusters
2. by species
3. by sex</p>
<div class="sourceCode" id="cb48"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb48-1"><a href="module-1-exercise-results.html#cb48-1" aria-hidden="true" tabindex="-1"></a><span class="fu">pairs</span>(</span>
<span id="cb48-2"><a href="module-1-exercise-results.html#cb48-2" aria-hidden="true" tabindex="-1"></a> crabs_meas, </span>
<span id="cb48-3"><a href="module-1-exercise-results.html#cb48-3" aria-hidden="true" tabindex="-1"></a> <span class="at">col =</span> <span class="fu">c</span>(<span class="st">"orchid"</span>,<span class="st">"forestgreen"</span>)[c_clusters]</span>
<span id="cb48-4"><a href="module-1-exercise-results.html#cb48-4" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
<p><img src="bookdown-demo_files/figure-html/unnamed-chunk-23-1.png" width="672" /></p>
<div class="sourceCode" id="cb49"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb49-1"><a href="module-1-exercise-results.html#cb49-1" aria-hidden="true" tabindex="-1"></a><span class="fu">pairs</span>(</span>
<span id="cb49-2"><a href="module-1-exercise-results.html#cb49-2" aria-hidden="true" tabindex="-1"></a> crabs_meas, </span>
<span id="cb49-3"><a href="module-1-exercise-results.html#cb49-3" aria-hidden="true" tabindex="-1"></a> <span class="at">col =</span> <span class="fu">c</span>(<span class="st">"orchid"</span>,<span class="st">"forestgreen"</span>)[<span class="fu">factor</span>(crabs<span class="sc">$</span>sp)]</span>
<span id="cb49-4"><a href="module-1-exercise-results.html#cb49-4" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
<p><img src="bookdown-demo_files/figure-html/unnamed-chunk-23-2.png" width="672" /></p>
<div class="sourceCode" id="cb50"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb50-1"><a href="module-1-exercise-results.html#cb50-1" aria-hidden="true" tabindex="-1"></a><span class="fu">pairs</span>(</span>
<span id="cb50-2"><a href="module-1-exercise-results.html#cb50-2" aria-hidden="true" tabindex="-1"></a> crabs_meas, </span>
<span id="cb50-3"><a href="module-1-exercise-results.html#cb50-3" aria-hidden="true" tabindex="-1"></a> <span class="at">col =</span> <span class="fu">c</span>(<span class="st">"orchid"</span>,<span class="st">"forestgreen"</span>)[<span class="fu">factor</span>(crabs<span class="sc">$</span>sex)]</span>
<span id="cb50-4"><a href="module-1-exercise-results.html#cb50-4" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
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