Updated bioc rendered

docs/labs/bioc/bioc_03_integration.html

@@ -207,7 +207,7 @@ <h1 class="title"><i class="fa-solid fa-diagram-project" aria-label="diagram-pro
       <div>
       <div class="quarto-title-meta-heading">Published</div>
       <div class="quarto-title-meta-contents">
-        <p class="date">30-Jan-2024</p>
+        <p class="date">05-Feb-2024</p>
       </div>
     </div>
 
@@ -316,12 +316,16 @@ <h2 data-number="1" class="anchored" data-anchor-id="meta-int_prep"><span class=
 <span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a>})</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <div class="cell">
-<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>path_data <span class="ot">&lt;-</span> <span class="st">"https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"</span></span>
-<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>path_file <span class="ot">&lt;-</span> <span class="st">"data/covid/results/bioc_covid_qc_dr.rds"</span></span>
-<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">dir.exists</span>(<span class="fu">dirname</span>(path_file))) <span class="fu">dir.create</span>(<span class="fu">dirname</span>(path_file), <span class="at">recursive =</span> <span class="cn">TRUE</span>)</span>
-<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">file.exists</span>(path_file)) <span class="fu">download.file</span>(<span class="at">url =</span> <span class="fu">file.path</span>(path_data, <span class="st">"covid/results/bioc_covid_qc_dr.rds"</span>), <span class="at">destfile =</span> path_file)</span>
-<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a>sce <span class="ot">&lt;-</span> <span class="fu">readRDS</span>(path_file)</span>
-<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">reducedDims</span>(sce))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="co"># download pre-computed data if missing or long compute</span></span>
+<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>fetch_data <span class="ot">&lt;-</span> <span class="cn">TRUE</span></span>
+<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="co"># url for source and intermediate data</span></span>
+<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a>path_data <span class="ot">&lt;-</span> <span class="st">"https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"</span></span>
+<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a>path_file <span class="ot">&lt;-</span> <span class="st">"data/covid/results/bioc_covid_qc_dr.rds"</span></span>
+<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">dir.exists</span>(<span class="fu">dirname</span>(path_file))) <span class="fu">dir.create</span>(<span class="fu">dirname</span>(path_file), <span class="at">recursive =</span> <span class="cn">TRUE</span>)</span>
+<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (fetch_data <span class="sc">&amp;&amp;</span> <span class="sc">!</span><span class="fu">file.exists</span>(path_file)) <span class="fu">download.file</span>(<span class="at">url =</span> <span class="fu">file.path</span>(path_data, <span class="st">"covid/results/bioc_covid_qc_dr.rds"</span>), <span class="at">destfile =</span> path_file)</span>
+<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a>sce <span class="ot">&lt;-</span> <span class="fu">readRDS</span>(path_file)</span>
+<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(<span class="fu">reducedDims</span>(sce))</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>List of length 8
 names(8): PCA UMAP tSNE_on_PCA ... UMAP_on_ScaleData KNN UMAP_on_Graph</code></pre>
@@ -565,6 +569,13 @@ <h2 data-number="3" class="anchored" data-anchor-id="meta-dimred_scanorama"><spa
 <span id="cb20-16"><a href="#cb20-16" aria-hidden="true" tabindex="-1"></a>sce <span class="ot">&lt;-</span> <span class="fu">runUMAP</span>(sce, <span class="at">dimred =</span> <span class="st">"Scanorama_PCA"</span>, <span class="at">n_dimred =</span> <span class="dv">50</span>, <span class="at">ncomponents =</span> <span class="dv">2</span>, <span class="at">name =</span> <span class="st">"UMAP_on_Scanorama"</span>)</span>
 <span id="cb20-17"><a href="#cb20-17" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb20-18"><a href="#cb20-18" aria-hidden="true" tabindex="-1"></a><span class="fu">plotReducedDim</span>(sce, <span class="at">dimred =</span> <span class="st">"UMAP_on_Scanorama"</span>, <span class="at">colour_by =</span> <span class="st">"sample"</span>, <span class="at">point_size =</span> <span class="fl">0.6</span>) <span class="sc">+</span> ggplot2<span class="sc">::</span><span class="fu">ggtitle</span>(<span class="at">label =</span> <span class="st">"UMAP_on_Scanorama"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="cell-output-display">
+<div class="quarto-figure quarto-figure-left">
+<figure class="figure">
+<p><a href="bioc_03_integration_files/figure-html/unnamed-chunk-13-1.png" class="lightbox" data-gallery="quarto-lightbox-gallery-5"><img src="bioc_03_integration_files/figure-html/unnamed-chunk-13-1.png" class="img-fluid figure-img" width="1440"></a></p>
+</figure>
+</div>
+</div>
 </div>
 </section>
 <section id="overview-all-methods" class="level2" data-number="4">
@@ -578,6 +589,13 @@ <h2 data-number="4" class="anchored" data-anchor-id="overview-all-methods"><span
 <span id="cb21-5"><a href="#cb21-5" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb21-6"><a href="#cb21-6" aria-hidden="true" tabindex="-1"></a><span class="fu">wrap_plots</span>(p1, p2, p3, p4, <span class="at">nrow =</span> <span class="dv">2</span>) <span class="sc">+</span></span>
 <span id="cb21-7"><a href="#cb21-7" aria-hidden="true" tabindex="-1"></a>    <span class="fu">plot_layout</span>(<span class="at">guides =</span> <span class="st">"collect"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="cell-output-display">
+<div class="quarto-figure quarto-figure-left">
+<figure class="figure">
+<p><a href="bioc_03_integration_files/figure-html/unnamed-chunk-14-1.png" class="lightbox" data-gallery="quarto-lightbox-gallery-6"><img src="bioc_03_integration_files/figure-html/unnamed-chunk-14-1.png" class="img-fluid figure-img" width="960"></a></p>
+</figure>
+</div>
+</div>
 </div>
 <p>Let’s save the integrated data for further analysis.</p>
 <div class="cell">
@@ -920,10 +938,11 @@ <h2 data-number="5" class="anchored" data-anchor-id="meta-session"><span class="
     <div class="nav-footer-center">
       &nbsp;
     </div>
-    <div class="nav-footer-right">Published with <a href="https://quarto.org/">Quarto</a> v1.3.450</div>
+    <div class="nav-footer-right">Published with <a href="https://quarto.org/">Quarto</a> v1.3.450
+</div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"selector":".lightbox","loop":true,"descPosition":"bottom","closeEffect":"zoom","openEffect":"zoom"});</script>
+<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","selector":".lightbox","openEffect":"zoom","loop":true,"closeEffect":"zoom"});</script>