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Quarto GHA Workflow Runner committed Jun 14, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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2 changes: 1 addition & 1 deletion 1_setup.html
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Expand Up @@ -282,7 +282,7 @@ <h1 class="title">Setup</h1>
4 directories, 16 files</code></pre>
<p>This data is provided by 10x genomics, and further information, like material and methods can be found here:</p>
<ul>
<li>Antherior: <a href="https://www.10xgenomics.com/datasets/mouse-brain-serial-section-1-sagittal-anterior-1-standard-1-1-0">https://www.10xgenomics.com/datasets/mouse-brain-serial-section-1-sagittal-anterior-1-standard-1-1-0</a>
<li>Anterior: <a href="https://www.10xgenomics.com/datasets/mouse-brain-serial-section-1-sagittal-anterior-1-standard-1-1-0">https://www.10xgenomics.com/datasets/mouse-brain-serial-section-1-sagittal-anterior-1-standard-1-1-0</a>
</li>
<li>Posterior: <a href="https://www.10xgenomics.com/datasets/mouse-brain-serial-section-1-sagittal-posterior-1-standard-1-1-0">https://www.10xgenomics.com/datasets/mouse-brain-serial-section-1-sagittal-posterior-1-standard-1-1-0</a>
</li>
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14 changes: 11 additions & 3 deletions 2_quality_control.html
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Expand Up @@ -556,7 +556,11 @@ <h1 class="title">Quality control</h1>
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="co"># defining the high mt spot in anterior</span></span>
<span><span class="va">seu</span><span class="op">$</span><span class="va">percent_mt_keep</span> <span class="op">&lt;-</span> <span class="op">!</span><span class="op">(</span><span class="va">seu</span><span class="op">$</span><span class="va">orig.ident</span> <span class="op">==</span> <span class="st">"Anterior"</span> <span class="op">&amp;</span> <span class="va">seu</span><span class="op">$</span><span class="va">percent_mt</span> <span class="op">&gt;</span> <span class="fl">38</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://satijalab.org/seurat/reference/SpatialPlot.html">SpatialPlot</a></span><span class="op">(</span><span class="va">seu</span>, group.by <span class="op">=</span> <span class="st">"percent_mt_keep"</span><span class="op">)</span> <span class="op">+</span></span>
<span><span class="va">cells_mt_keep</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html">colnames</a></span><span class="op">(</span><span class="va">seu</span><span class="op">)</span><span class="op">[</span><span class="va">seu</span><span class="op">$</span><span class="va">percent_mt_keep</span><span class="op">]</span></span>
<span></span>
<span><span class="fu"><a href="https://satijalab.org/seurat/reference/SpatialPlot.html">SpatialPlot</a></span><span class="op">(</span><span class="va">seu</span>, cells.highlight <span class="op">=</span> <span class="va">cells_mt_keep</span>,</span>
<span> cols.highlight <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"grey50"</span>, <span class="st">"red"</span><span class="op">)</span>,</span>
<span> pt.size.factor <span class="op">=</span> <span class="fl">2.5</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://patchwork.data-imaginist.com/reference/plot_annotation.html">plot_annotation</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"Filter % mitochondrial UMI"</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://patchwork.data-imaginist.com/reference/plot_layout.html">plot_layout</a></span><span class="op">(</span>guides<span class="op">=</span><span class="st">'collect'</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html">theme</a></span><span class="op">(</span>legend.position <span class="op">=</span> <span class="st">"none"</span><span class="op">)</span> </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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Expand All @@ -568,9 +572,13 @@ <h1 class="title">Quality control</h1>
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="co"># defining the low number of genes</span></span>
<span><span class="va">seu</span><span class="op">$</span><span class="va">nFeature_Spatial_keep</span> <span class="op">&lt;-</span> <span class="va">seu</span><span class="op">$</span><span class="va">nFeature_Spatial</span> <span class="op">&gt;</span> <span class="fl">100</span></span>
<span></span>
<span><span class="fu"><a href="https://satijalab.org/seurat/reference/SpatialPlot.html">SpatialPlot</a></span><span class="op">(</span><span class="va">seu</span>, group.by <span class="op">=</span> <span class="st">"nFeature_Spatial_keep"</span><span class="op">)</span> <span class="op">+</span></span>
<span><span class="va">cells_nfeature_keep</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html">colnames</a></span><span class="op">(</span><span class="va">seu</span><span class="op">)</span><span class="op">[</span><span class="va">seu</span><span class="op">$</span><span class="va">nFeature_Spatial_keep</span><span class="op">]</span></span>
<span></span>
<span><span class="fu"><a href="https://satijalab.org/seurat/reference/SpatialPlot.html">SpatialPlot</a></span><span class="op">(</span><span class="va">seu</span>, cells.highlight <span class="op">=</span> <span class="va">cells_nfeature_keep</span>,</span>
<span> cols.highlight <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"grey50"</span>, <span class="st">"red"</span><span class="op">)</span>,</span>
<span> pt.size.factor <span class="op">=</span> <span class="fl">2.5</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://patchwork.data-imaginist.com/reference/plot_annotation.html">plot_annotation</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"Filter % low number of features"</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://patchwork.data-imaginist.com/reference/plot_layout.html">plot_layout</a></span><span class="op">(</span>guides<span class="op">=</span><span class="st">'collect'</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html">theme</a></span><span class="op">(</span>legend.position <span class="op">=</span> <span class="st">"none"</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span> <span class="fu"><a href="https://patchwork.data-imaginist.com/reference/plot_layout.html">plot_layout</a></span><span class="op">(</span>guides<span class="op">=</span><span class="st">'collect'</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme.html">theme</a></span><span class="op">(</span>legend.position <span class="op">=</span> <span class="st">"none"</span><span class="op">)</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>
<figure class="figure"><p><img src="2_quality_control_files/figure-html/unnamed-chunk-15-2.png" class="img-fluid figure-img" width="672"></p>
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