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Reorganise tutorial files
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@RiboRings
RiboRings committed Jun 7, 2024
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222 changes: 168 additions & 54 deletions docs/tengeler_alpha_diversity.html → docs/alpha_diversity.html
100755 → 100644
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.0.38">
<meta name="generator" content="quarto-1.3.450">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand All @@ -11,10 +11,16 @@
<style>
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padding: 0 4px; width: 4em;
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"search-more-matches-text": "more matches in this document",
"search-clear-button-title": "Clear",
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"search-submit-button-title": "Submit"
"search-submit-button-title": "Submit",
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Expand Down Expand Up @@ -140,6 +117,7 @@ <h1 class="title">Alpha Diversity</h1>
<div class="quarto-title-meta">




</div>

Expand Down Expand Up @@ -207,8 +185,8 @@ <h2 class="anchored" data-anchor-id="visualisation">Visualisation</h2>
<div class="cell-output-display">
<div id="fig-alpha" class="quarto-figure quarto-figure-center anchored">
<figure class="figure">
<p><img src="tengeler_alpha_diversity_files/figure-html/fig-alpha-1.png" class="img-fluid figure-img" width="768"></p>
<p></p><figcaption class="figure-caption">Figure 1: Box plots of (A) coverage (B) Shannon and (C) inverse Simpson indices grouped by patient status and coloured by cohort.</figcaption><p></p>
<p><img src="alpha_diversity_files/figure-html/fig-alpha-1.png" class="img-fluid figure-img" width="768"></p>
<figcaption class="figure-caption">Figure&nbsp;1: Box plots of (A) coverage (B) Shannon and (C) inverse Simpson indices grouped by patient status and coloured by cohort.</figcaption>
</figure>
</div>
</div>
Expand Down Expand Up @@ -245,9 +223,23 @@ <h2 class="anchored" data-anchor-id="visualisation">Visualisation</h2>
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Expand All @@ -259,7 +251,24 @@ <h2 class="anchored" data-anchor-id="visualisation">Visualisation</h2>
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Expand Down Expand Up @@ -287,31 +296,136 @@ <h2 class="anchored" data-anchor-id="visualisation">Visualisation</h2>
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20 changes: 6 additions & 14 deletions docs/bioconductor.html
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Expand Up @@ -8,7 +8,7 @@
<link href="site_libs/quarto-html/light-border.css" rel="stylesheet">
<link href="site_libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
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<title>Bioconductor</title>
<meta name="apple-mobile-web-app-capable" content="yes">
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}

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Expand Down Expand Up @@ -455,6 +454,7 @@ <h2>R/Bioc community</h2>
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Expand Down Expand Up @@ -715,9 +715,10 @@ <h2>R/Bioc community</h2>
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Expand All @@ -727,17 +728,8 @@ <h2>R/Bioc community</h2>
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6 changes: 3 additions & 3 deletions docs/tengeler_community_composition.html → docs/compositional_heatmap.html
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Expand Up @@ -444,7 +444,7 @@ <h2>Why relative abundances?</h2>
</details>

</div>
<img data-src="tengeler_community_composition_files/figure-revealjs/fig-abund-1.png" width="960" class="r-stretch quarto-figure-center"><p class="caption">Figure&nbsp;1: Sample composition by counts (left) or relative abundance (right).</p></section>
<img data-src="compositional_heatmap_files/figure-revealjs/fig-abund-1.png" width="960" class="r-stretch quarto-figure-center"><p class="caption">Figure&nbsp;1: Sample composition by counts (left) or relative abundance (right).</p></section>
<section id="example-1.2" class="slide level2">
<h2>Example 1.2</h2>
<p>To reduce data skewness, we further transform the relative abundance assay with the <strong>Centered-Log Ratio</strong> (CLR), which is defined as follows:</p>
Expand Down Expand Up @@ -479,7 +479,7 @@ <h2>Example 1.3</h2>
<span id="cb8-3"><a href="#cb8-3"></a>clrz_hm</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>
<img data-src="tengeler_community_composition_files/figure-revealjs/fig-compheat-1.png" width="960" class="r-stretch quarto-figure-center"><p class="caption">Figure&nbsp;2: Heatmap of CLR-Z assay where columns correspond to samples and rows to taxa agglomerated by order.</p></section>
<img data-src="compositional_heatmap_files/figure-revealjs/fig-compheat-1.png" width="960" class="r-stretch quarto-figure-center"><p class="caption">Figure&nbsp;2: Heatmap of CLR-Z assay where columns correspond to samples and rows to taxa agglomerated by order.</p></section>
<section id="why-clr-z-transformation" class="slide level2">
<h2>Why clr-z transformation?</h2>
<p>A CLR-z transformation improves comparability in two steps:</p>
Expand All @@ -488,7 +488,7 @@ <h2>Why clr-z transformation?</h2>
<li>Find <strong>Z score</strong> to standardise features <strong>row-wise</strong></li>
</ol>

<img data-src="tengeler_community_composition_files/figure-revealjs/fig-comparison-1.png" width="960" class="r-stretch quarto-figure-center"><p class="caption">Figure&nbsp;3: Visual comparison between counts, relative abundance, clr and clr-z assays (from left to right).</p></section>
<img data-src="compositional_heatmap_files/figure-revealjs/fig-comparison-1.png" width="960" class="r-stretch quarto-figure-center"><p class="caption">Figure&nbsp;3: Visual comparison between counts, relative abundance, clr and clr-z assays (from left to right).</p></section>
<section id="exercise-1" class="slide level2">
<h2>Exercise 1</h2>
<ul>
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0 ...iles/figure-revealjs/fig-comparison-1.png → ...iles/figure-revealjs/fig-comparison-1.png
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0 ..._files/figure-revealjs/fig-compheat-1.png → ..._files/figure-revealjs/fig-compheat-1.png
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