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MiqG committed Mar 17, 2024
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36 changes: 31 additions & 5 deletions 01-intro_to_tidyverse.html
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<script>DOCUMENTATION_OPTIONS.pagename = '01-intro_to_tidyverse';</script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
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<li class="toctree-l1 current active"><a class="current reference internal" href="#">What is the Tidyverse?</a></li>





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<li class="toctree-l1"><a class="reference internal" href="03-bio.html">Biology-related data visualization</a></li>
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<li class="toctree-l1"><a class="reference internal" href="04-exercise.html">Exploratory Data Analysis of the most popular human gene</a></li>

<li class="toctree-l1"><a class="reference internal" href="04-bio.html">Biology-related data visualization</a></li>




<li class="toctree-l1"><a class="reference internal" href="05-exercise.html">Exploratory Data Analysis of the most popular human gene</a></li>



Expand Down Expand Up @@ -913,6 +921,24 @@ <h1>Session Info<a class="headerlink" href="#session-info" title="Permalink to t
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<script>DOCUMENTATION_OPTIONS.pagename = '02-intro';</script>
<link rel="index" title="Index" href="genindex.html" />
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<ul class="nav bd-sidenav">
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<li class="toctree-l1"><a class="reference internal" href="04-exercise.html">Exploratory Data Analysis of the most popular human gene</a></li>

<li class="toctree-l1"><a class="reference internal" href="04-bio.html">Biology-related data visualization</a></li>




<li class="toctree-l1"><a class="reference internal" href="05-exercise.html">Exploratory Data Analysis of the most popular human gene</a></li>



Expand Down Expand Up @@ -457,49 +465,49 @@ <h2>How many penguins of each species did we observe in total?<a class="headerli
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ggpie(dat %&gt;% count(species), x = &quot;n&quot;, fill = &quot;species&quot;)
</pre></div>
</div>
<p><img alt="" src="_images/unnamed-chunk-3-11.png" /></p>
<p><img alt="" src="_images/unnamed-chunk-3-1.png" /></p>
</div>
<div class="section" id="how-many-penguins-of-each-species-and-sex-did-we-observe-across-the-different-islands">
<h2>How many penguins of each species and sex did we observe across the different islands?<a class="headerlink" href="#how-many-penguins-of-each-species-and-sex-did-we-observe-across-the-different-islands" title="Permalink to this heading">#</a></h2>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ggbarplot(dat %&gt;% count(species, sex, island), x = &quot;species&quot;, y = &quot;n&quot;, fill = &quot;sex&quot;,
label = TRUE, position = position_dodge(0.7), facet.by = &quot;island&quot;, palette = &quot;lancet&quot;)
</pre></div>
</div>
<p><img alt="" src="_images/unnamed-chunk-4-11.png" /></p>
<p><img alt="" src="_images/unnamed-chunk-4-1.png" /></p>
</div>
<div class="section" id="what-are-the-distributions-of-flipper-lengths-considering-penguin-species-sex-and-islands-of-origin">
<h2>What are the distributions of flipper lengths considering penguin species, sex and islands of origin?<a class="headerlink" href="#what-are-the-distributions-of-flipper-lengths-considering-penguin-species-sex-and-islands-of-origin" title="Permalink to this heading">#</a></h2>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>gghistogram(dat, x = &quot;flipper_length_mm&quot;, fill = &quot;sex&quot;, facet.by = c(&quot;species&quot;,&quot;island&quot;))
</pre></div>
</div>
<p><img alt="" src="_images/unnamed-chunk-5-11.png" /></p>
<p><img alt="" src="_images/unnamed-chunk-5-1.png" /></p>
<p>Alternatively, we can use stripcharts charts:</p>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ggstripchart(dat, x = &quot;island&quot;, y = &quot;flipper_length_mm&quot;, color = &quot;sex&quot;, facet.by = &quot;species&quot;, alpha = 0.5, position = position_jitterdodge(), add = &quot;median_iqr&quot;, add.params = list(color=&quot;black&quot;, group=&quot;sex&quot;, size=0.2))
</pre></div>
</div>
<p><img alt="" src="_images/unnamed-chunk-6-11.png" /></p>
<p><img alt="" src="_images/unnamed-chunk-6-1.png" /></p>
</div>
<div class="section" id="are-the-differences-of-body-mass-between-sexes-significant-if-we-control-for-species-and-island">
<h2>Are the differences of body mass between sexes significant if we control for species and island?<a class="headerlink" href="#are-the-differences-of-body-mass-between-sexes-significant-if-we-control-for-species-and-island" title="Permalink to this heading">#</a></h2>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ggstripchart(dat, x = &quot;island&quot;, y = &quot;body_mass_g&quot;, color = &quot;sex&quot;, facet.by = &quot;species&quot;, alpha = 0.5, position = position_jitterdodge(), add = &quot;median_iqr&quot;, add.params = list(color=&quot;black&quot;, group=&quot;sex&quot;, size=0.2))+
stat_compare_means(aes(color = sex), label = &quot;p.signif&quot;, method = &quot;wilcox.test&quot;)
</pre></div>
</div>
<p><img alt="" src="_images/unnamed-chunk-7-11.png" /></p>
<p><img alt="" src="_images/unnamed-chunk-7-1.png" /></p>
</div>
<div class="section" id="what-is-the-relationship-between-flipper-length-body-mass-and-bill-length">
<h2>What is the relationship between flipper length, body mass and bill length?<a class="headerlink" href="#what-is-the-relationship-between-flipper-length-body-mass-and-bill-length" title="Permalink to this heading">#</a></h2>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ggscatter(dat, x = &quot;flipper_length_mm&quot;, y = &quot;body_mass_g&quot;, color = &quot;bill_length_mm&quot;, alpha = 0.5)
</pre></div>
</div>
<p><img alt="" src="_images/unnamed-chunk-8-11.png" /></p>
<p><img alt="" src="_images/unnamed-chunk-8-1.png" /></p>
</div>
<div class="section" id="could-we-have-sampling-bias-in-the-relationship-between-flipper-length-and-body-mass">
<h2>Could we have sampling bias in the relationship between flipper length and body mass?<a class="headerlink" href="#could-we-have-sampling-bias-in-the-relationship-between-flipper-length-and-body-mass" title="Permalink to this heading">#</a></h2>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>ggscatter(dat %&gt;% mutate(year=factor(year)), x = &quot;flipper_length_mm&quot;, y = &quot;body_mass_g&quot;, alpha = 0.5, color = &quot;year&quot;, ellipse = TRUE)
</pre></div>
</div>
<p><img alt="" src="_images/unnamed-chunk-9-11.png" /></p>
<p><img alt="" src="_images/unnamed-chunk-9-1.png" /></p>
</div>
<div class="section" id="what-is-the-spearman-correlation-coefficient-between-body-mass-and-flipper-length">
<h2>What is the spearman correlation coefficient between body mass and flipper length?<a class="headerlink" href="#what-is-the-spearman-correlation-coefficient-between-body-mass-and-flipper-length" title="Permalink to this heading">#</a></h2>
Expand All @@ -510,7 +518,7 @@ <h2>What is the spearman correlation coefficient between body mass and flipper l
theme(aspect.ratio = 1)
</pre></div>
</div>
<p><img alt="" src="_images/unnamed-chunk-10-11.png" /></p>
<p><img alt="" src="_images/unnamed-chunk-10-1.png" /></p>
</div>
<div class="section" id="create-and-save-a-figure">
<h2>Create and save a figure<a class="headerlink" href="#create-and-save-a-figure" title="Permalink to this heading">#</a></h2>
Expand Down Expand Up @@ -577,7 +585,7 @@ <h1>Heatmaps with <code class="docutils literal notranslate"><span class="pre">C
right_annotation = annotation_row)
</pre></div>
</div>
<p><img alt="" src="_images/unnamed-chunk-12-11.png" /></p>
<p><img alt="" src="_images/unnamed-chunk-12-1.png" /></p>
</div>
<div class="section" id="references">
<h1>References<a class="headerlink" href="#references" title="Permalink to this heading">#</a></h1>
Expand Down Expand Up @@ -682,6 +690,24 @@ <h1>Session Info<a class="headerlink" href="#session-info" title="Permalink to t
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