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Quarto GHA Workflow Runner committed Apr 30, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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2 changes: 1 addition & 1 deletion index-preview.html
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Expand Up @@ -1986,7 +1986,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
}
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</script> </div> <!-- /content --> <script>var lightboxQuarto = GLightbox({"openEffect":"zoom","loop":false,"closeEffect":"zoom","descPosition":"bottom","selector":".lightbox"});
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window.onload = () => {
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44 changes: 22 additions & 22 deletions index.embed.ipynb
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2 changes: 1 addition & 1 deletion index.html
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Expand Up @@ -974,7 +974,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
});
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<script>var lightboxQuarto = GLightbox({"selector":".lightbox","closeEffect":"zoom","loop":false,"openEffect":"zoom","descPosition":"bottom"});
<script>var lightboxQuarto = GLightbox({"selector":".lightbox","loop":false,"closeEffect":"zoom","openEffect":"zoom","descPosition":"bottom"});
window.onload = () => {
lightboxQuarto.on('slide_before_load', (data) => {
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44 changes: 22 additions & 22 deletions index.out.ipynb
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64 changes: 63 additions & 1 deletion notebooks/TCGA-preview.html
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<script src="../site_libs/bootstrap/bootstrap.min.js"></script>
<link href="../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
<link href="../site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
<script src="../site_libs/quarto-contrib/glightbox/glightbox.min.js"></script>
<link href="../site_libs/quarto-contrib/glightbox/glightbox.min.css" rel="stylesheet">
<link href="../site_libs/quarto-contrib/glightbox/lightbox.css" rel="stylesheet">
<script async="" src="https://hypothes.is/embed.js"></script>
<script>
window.document.addEventListener("DOMContentLoaded", function (_event) {
Expand Down Expand Up @@ -1174,6 +1177,41 @@ <h2 class="anchored" data-anchor-id="analyzing-mutation-data">Analyzing Mutation
</div>
</div></div>
<p>We can visualize the most common mutated genes genes in rectum adenocarcinoma</p>
<div class="cell-container"><div class="cell-decorator"><pre>In [18]:</pre></div><div id="cell-fig-genesmut" class="cell">
<div class="sourceCode cell-code" id="cb152"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb152-1"><a href="#cb152-1" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb152-2"><a href="#cb152-2" aria-hidden="true" tabindex="-1"></a>p <span class="ot">&lt;-</span> var_class_df <span class="sc">|&gt;</span> </span>
<span id="cb152-3"><a href="#cb152-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">as_tibble</span>() <span class="sc">|&gt;</span> </span>
<span id="cb152-4"><a href="#cb152-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(symbol,variant_class) <span class="sc">|&gt;</span> </span>
<span id="cb152-5"><a href="#cb152-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarise</span>(<span class="at">n =</span> <span class="fu">n</span>()) <span class="sc">|&gt;</span> </span>
<span id="cb152-6"><a href="#cb152-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">arrange</span>(<span class="fu">desc</span>(n)) <span class="sc">|&gt;</span> </span>
<span id="cb152-7"><a href="#cb152-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">ungroup</span>() <span class="sc">|&gt;</span> </span>
<span id="cb152-8"><a href="#cb152-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">slice_max</span>(<span class="at">order_by =</span> n, <span class="at">n =</span> <span class="dv">20</span>) <span class="sc">|&gt;</span> </span>
<span id="cb152-9"><a href="#cb152-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">ungroup</span>() <span class="sc">|&gt;</span> </span>
<span id="cb152-10"><a href="#cb152-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">symbol =</span> <span class="fu">fct_reorder</span>(symbol,n)) <span class="sc">|&gt;</span> </span>
<span id="cb152-11"><a href="#cb152-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(n, symbol,<span class="at">fill=</span>variant_class)) <span class="sc">+</span></span>
<span id="cb152-12"><a href="#cb152-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_col</span>() <span class="sc">+</span></span>
<span id="cb152-13"><a href="#cb152-13" aria-hidden="true" tabindex="-1"></a> <span class="fu">facet_wrap</span>(<span class="sc">~</span>variant_class) <span class="sc">+</span></span>
<span id="cb152-14"><a href="#cb152-14" aria-hidden="true" tabindex="-1"></a> paletteer<span class="sc">::</span><span class="fu">scale_fill_paletteer_d</span>(<span class="st">"awtools::a_palette"</span>) <span class="sc">+</span></span>
<span id="cb152-15"><a href="#cb152-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(<span class="at">x =</span> <span class="st">"Samples with specific mutation"</span>, <span class="at">y=</span><span class="st">"Gene Symbol"</span>, <span class="at">fill=</span><span class="st">"Variant Class"</span>,</span>
<span id="cb152-16"><a href="#cb152-16" aria-hidden="true" tabindex="-1"></a> <span class="at">title=</span><span class="st">"Top 20 Samples with READ"</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-stderr">
<pre><code>`summarise()` has grouped output by 'symbol'. You can override using the
`.groups` argument.</code></pre>
</div>
<div class="sourceCode cell-code" id="cb154"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb154-1"><a href="#cb154-1" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb154-2"><a href="#cb154-2" aria-hidden="true" tabindex="-1"></a>path <span class="ot">&lt;-</span> <span class="st">"images/"</span></span>
<span id="cb154-3"><a href="#cb154-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb154-4"><a href="#cb154-4" aria-hidden="true" tabindex="-1"></a><span class="fu">ggsave</span>(<span class="fu">paste0</span>(path,<span class="st">"samples_with_mut.jpeg"</span>), <span class="at">device =</span> <span class="st">"jpeg"</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-stderr">
<pre><code>Saving 7 x 5 in image</code></pre>
</div>
</div></div>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><a href="images/samples_with_mut.jpeg" class="lightbox" data-gallery="quarto-lightbox-gallery-1" title="Samples with specific mutation per gene"><img src="images/samples_with_mut.jpeg" class="img-fluid figure-img" alt="Samples with specific mutation per gene"></a></p>
<figcaption>Samples with specific mutation per gene</figcaption>
</figure>
</div>
</section>
</main>
<!-- /main column --> <script id="quarto-html-after-body" type="application/javascript">
Expand Down Expand Up @@ -1595,6 +1633,30 @@ <h2 class="anchored" data-anchor-id="analyzing-mutation-data">Analyzing Mutation
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</body></html>
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