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<h1 class="title toc-ignore">Zeisel expert-annotated marker gene analysis</h1>
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<strong>Last updated:</strong> 2022-05-02
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<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 7 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 0
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<strong>Knit directory:</strong> <code>mage_2020_marker-gene-benchmarking/</code> <span class="glyphicon glyphicon-question-sign" aria-hidden="true" title="This is the local directory in which the code in this file was executed."> </span>
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This reproducible <a href="https://rmarkdown.rstudio.com">R Markdown</a> analysis was created with <a
href="https://github.com/workflowr/workflowr">workflowr</a> (version 1.7.0). The <em>Checks</em> tab describes the reproducibility checks that were applied when the results were created. The <em>Past versions</em> tab lists the development history.
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRMarkdownfilestronguptodate"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>R Markdown file:</strong> up-to-date </a>
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<p>Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.</p>
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<p>Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.</p>
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<p>The command <code>set.seed(20190102)</code> was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.</p>
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<p>Great job! Recording the operating system, R version, and package versions is critical for reproducibility.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongFilepathsstrongrelative"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>File paths:</strong> relative </a>
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<p>Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.</p>
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(dplyr)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(SingleCellExperiment)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(scater)</span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyr)</span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(forcats)</span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(patchwork)</span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"code"</span>, <span class="st">"analysis-utils.R"</span>))</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"code"</span>, <span class="st">"plot-utils.R"</span>))</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"code"</span>, <span class="st">"expert-annotation-utils.R"</span>))</span></code></pre></div>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>zeisel_results <span class="ot"><-</span> <span class="fu">load_real_data_results</span>(<span class="st">"zeisel"</span>)</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>zeisel <span class="ot"><-</span> <span class="fu">readRDS</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data"</span>, <span class="st">"special_real_data"</span>, <span class="st">"zeisel.rds"</span>))</span></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>zeisel_marker_genes <span class="ot"><-</span> <span class="fu">tribble</span>(</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a> <span class="sc">~</span>cluster, <span class="sc">~</span>expert_mgs,</span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"interneurons"</span>, <span class="st">"Pnoc"</span>,</span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a> <span class="st">"pyramidal SS"</span>, <span class="st">"Tbr1"</span>,</span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a> <span class="st">"pyramidal CA1"</span>, <span class="st">"Spink8"</span>,</span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a> <span class="st">"oligodendrocytes"</span>, <span class="st">"Hapln2"</span>,</span>
<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a> <span class="st">"microglia"</span>, <span class="st">"Aif1"</span>,</span>
<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a> <span class="st">"endothelial-mural"</span>, <span class="st">"Acta2"</span>, </span>
<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a> <span class="st">"astrocytes_ependymal"</span>, <span class="st">"Aldoc"</span></span>
<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a>) </span></code></pre></div>
<div id="genes" class="section level1">
<h1>10 genes</h1>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">plot_expert_anno_heatmap</span>(</span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> zeisel_results, </span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"zeisel"</span>, </span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a> zeisel_marker_genes, </span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a> <span class="at">metric =</span> <span class="st">"recall"</span>, </span>
<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a> <span class="at">n_top =</span> <span class="dv">10</span></span>
<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
<p><img src="figure/zeisel-expert-analysis.Rmd/zeisel-10-genes-heatmap-1.svg" width="672" style="display: block; margin: auto;" /></p>
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<div id="genes-1" class="section level1">
<h1>20 genes</h1>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>expert_zeisel_heatmap <span class="ot"><-</span> <span class="fu">plot_expert_anno_heatmap</span>(</span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> zeisel_results, </span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"zeisel"</span>, </span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a> zeisel_marker_genes, </span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a> <span class="at">metric =</span> <span class="st">"recall"</span>, </span>
<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a> <span class="at">n_top =</span> <span class="dv">20</span></span>
<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a>expert_zeisel_heatmap</span></code></pre></div>
<p><img src="figure/zeisel-expert-analysis.Rmd/zeisel-30-genes-heatmap-1.svg" width="672" style="display: block; margin: auto;" /></p>
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<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/8b989e1e0553365ef45bb4cd5f80865c9639af43/public/figure/zeisel-expert-analysis.Rmd/zeisel-30-genes-heatmap-1.svg" target="_blank">8b989e1</a>
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<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="fu">saveRDS</span>(</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a> expert_zeisel_heatmap, </span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"figures"</span>, <span class="st">"raw"</span>, <span class="st">"expert-zeisel-heatmap.rds"</span>)</span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
</div>
<div id="expert-marker-genes" class="section level1">
<h1>Expert marker genes</h1>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="fu">plotExpression</span>(zeisel, <span class="at">x =</span> <span class="st">"label"</span>, zeisel_marker_genes<span class="sc">$</span>expert_mgs) <span class="sc">+</span> </span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">angle =</span> <span class="dv">30</span>, <span class="at">hjust =</span> <span class="dv">1</span>))</span></code></pre></div>
<p><img src="figure/zeisel-expert-analysis.Rmd/unnamed-chunk-1-1.svg" width="672" style="display: block; margin: auto;" /></p>
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<div id="selected-oligodendrocytes-markers" class="section level1">
<h1>Selected oligodendrocytes markers</h1>
<p>Mog is a known marker</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>seurat_wilcox <span class="ot"><-</span> <span class="fu">readRDS</span>(</span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"results"</span>, <span class="st">"real_data"</span>, <span class="st">"zeisel-seurat_wilcox.rds"</span>)</span>
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb8-5"><a href="#cb8-5" aria-hidden="true" tabindex="-1"></a>top_mgs <span class="ot"><-</span> seurat_wilcox<span class="sc">$</span>result <span class="sc">%>%</span> </span>
<span id="cb8-6"><a href="#cb8-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(cluster <span class="sc">==</span> <span class="st">"oligodendrocytes"</span>) <span class="sc">%>%</span> </span>
<span id="cb8-7"><a href="#cb8-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">head</span>(<span class="at">n =</span> <span class="dv">10</span>) <span class="sc">%>%</span> </span>
<span id="cb8-8"><a href="#cb8-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">pull</span>(gene)</span>
<span id="cb8-9"><a href="#cb8-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb8-10"><a href="#cb8-10" aria-hidden="true" tabindex="-1"></a>seurat_wilcox_top_oligodedrocyte <span class="ot"><-</span> <span class="fu">plotExpression</span>(zeisel, <span class="at">x =</span> <span class="st">"label"</span>, top_mgs) <span class="sc">+</span> </span>
<span id="cb8-11"><a href="#cb8-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">angle =</span> <span class="dv">45</span>, <span class="at">hjust =</span> <span class="dv">1</span>))</span>
<span id="cb8-12"><a href="#cb8-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb8-13"><a href="#cb8-13" aria-hidden="true" tabindex="-1"></a>seurat_wilcox_top_oligodedrocyte</span></code></pre></div>
<p><img src="figure/zeisel-expert-analysis.Rmd/found-oligodendrocyte-markers-1.svg" width="672" style="display: block; margin: auto;" /></p>
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<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ggsave</span>(</span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"figures"</span>, <span class="st">"final"</span>, <span class="st">"seurat-wilcox-top-oligodencrocytes.pdf"</span>),</span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a> seurat_wilcox_top_oligodedrocyte,</span>
<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a> <span class="at">width =</span> <span class="dv">8</span>,</span>
<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a> <span class="at">height =</span> <span class="dv">8</span>,</span>
<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a> <span class="at">units =</span> <span class="st">"in"</span></span>
<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
</div>
<div id="selected-interneurons---seurat-t-test" class="section level1">
<h1>Selected interneurons - Seurat t-test</h1>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>seurat_t <span class="ot"><-</span> <span class="fu">readRDS</span>(</span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"results"</span>, <span class="st">"real_data"</span>, <span class="st">"zeisel-seurat_t.rds"</span>)</span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a>seurat_t<span class="sc">$</span>result <span class="sc">%>%</span> </span>
<span id="cb10-6"><a href="#cb10-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(cluster <span class="sc">==</span> <span class="st">"interneurons"</span>) <span class="sc">%>%</span> </span>
<span id="cb10-7"><a href="#cb10-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">print</span>(<span class="at">n =</span> <span class="dv">2</span>)</span></code></pre></div>
<pre><code># A tibble: 1,369 × 7
p_value p_value_adj cluster log_fc gene raw_statistic scaled_statistic
<dbl> <dbl> <fct> <dbl> <chr> <dbl> <dbl>
1 1.05e-221 2.11e-218 interneurons 0.977 Snap… 0 0
2 5.21e-216 1.04e-212 interneurons 1.84 Ndrg4 0 0
# … with 1,367 more rows</code></pre>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a>interneuron_seurat_t <span class="ot"><-</span> <span class="fu">plotExpression</span>(zeisel, <span class="at">x =</span> <span class="st">"label"</span>, <span class="fu">c</span>(<span class="st">"Snap25"</span>, <span class="st">"Ndrg4"</span>)) <span class="sc">+</span> </span>
<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">angle =</span> <span class="dv">45</span>, <span class="at">hjust =</span> <span class="dv">1</span>))</span>
<span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb12-4"><a href="#cb12-4" aria-hidden="true" tabindex="-1"></a>interneuron_seurat_t</span></code></pre></div>
<p><img src="figure/zeisel-expert-analysis.Rmd/not-found-seurat-t-interneurons-markers-1.svg" width="672" style="display: block; margin: auto;" /></p>
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<p>
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<div class="table-responsive">
<table class="table table-condensed table-hover">
<thead>
<tr>
<th>
Version
</th>
<th>
Author
</th>
<th>
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/8b989e1e0553365ef45bb4cd5f80865c9639af43/public/figure/zeisel-expert-analysis.Rmd/not-found-seurat-t-interneurons-markers-1.svg" target="_blank">8b989e1</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2022-05-02
</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<div id="selected-interneurons---scran-t-test-any" class="section level1">
<h1>Selected interneurons - Scran t-test any</h1>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>scran_t_any <span class="ot"><-</span> <span class="fu">readRDS</span>(</span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a> here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"results"</span>, <span class="st">"real_data"</span>, <span class="st">"zeisel-scran_t_any.rds"</span>)</span>
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a>)</span>