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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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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenprivatemage2020markergenebenchmarkingtree14fb2518179907d20c594baef0d3922899e39398targetblank14fb251a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/tree/14fb2518179907d20c594baef0d3922899e39398" target="_blank">14fb251</a> </a>
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Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
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The results in this page were generated with repository version <a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/tree/14fb2518179907d20c594baef0d3922899e39398" target="_blank">14fb251</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
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Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
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<pre><code>
Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    .snakemake/
    Ignored:    NSForest/.Rhistory
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Unstaged changes:
    Modified:   analysis/about.Rmd
    Modified:   analysis/concordance.Rmd
    Modified:   analysis/double-dipping-analysis.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/lawlor-expert-analysis.Rmd
    Modified:   analysis/p-value-analysis.Rmd
    Modified:   analysis/pbmc3k-expert-analysis.Rmd
    Modified:   analysis/t-test-only-zero-case-study.Rmd
    Modified:   analysis/tpr.Rmd
    Modified:   code/expert-annotation-utils.R
    Modified:   code/manuscript-figures.R
    Modified:   code/plot-utils.R
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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">&quot;code&quot;</span>, <span class="st">&quot;analysis-utils.R&quot;</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">&quot;code&quot;</span>, <span class="st">&quot;plot-utils.R&quot;</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">&quot;code&quot;</span>, <span class="st">&quot;expert-annotation-utils.R&quot;</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">&lt;-</span> <span class="fu">load_real_data_results</span>(<span class="st">&quot;zeisel&quot;</span>)</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>zeisel <span class="ot">&lt;-</span> <span class="fu">readRDS</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;data&quot;</span>, <span class="st">&quot;special_real_data&quot;</span>, <span class="st">&quot;zeisel.rds&quot;</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">&lt;-</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">&quot;interneurons&quot;</span>,       <span class="st">&quot;Pnoc&quot;</span>,</span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a>          <span class="st">&quot;pyramidal SS&quot;</span>,       <span class="st">&quot;Tbr1&quot;</span>,</span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a>         <span class="st">&quot;pyramidal CA1&quot;</span>,     <span class="st">&quot;Spink8&quot;</span>,</span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a>      <span class="st">&quot;oligodendrocytes&quot;</span>,     <span class="st">&quot;Hapln2&quot;</span>,</span>
<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a>             <span class="st">&quot;microglia&quot;</span>,       <span class="st">&quot;Aif1&quot;</span>,</span>
<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a>     <span class="st">&quot;endothelial-mural&quot;</span>,      <span class="st">&quot;Acta2&quot;</span>, </span>
<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a>  <span class="st">&quot;astrocytes_ependymal&quot;</span>,      <span class="st">&quot;Aldoc&quot;</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">&quot;zeisel&quot;</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">&quot;recall&quot;</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>
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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">&lt;-</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">&quot;zeisel&quot;</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">&quot;recall&quot;</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>
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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">&quot;figures&quot;</span>, <span class="st">&quot;raw&quot;</span>, <span class="st">&quot;expert-zeisel-heatmap.rds&quot;</span>)</span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
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<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">&quot;label&quot;</span>, zeisel_marker_genes<span class="sc">$</span>expert_mgs) <span class="sc">+</span> </span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>    <span class="fu">theme</span>(<span class="at">axis.text.x =</span> <span class="fu">element_text</span>(<span class="at">angle =</span> <span class="dv">30</span>, <span class="at">hjust =</span> <span class="dv">1</span>))</span></code></pre></div>
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<div id="selected-oligodendrocytes-markers" class="section level1">
<h1>Selected oligodendrocytes markers</h1>
<p>Mog is a known marker</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>seurat_wilcox <span class="ot">&lt;-</span> <span class="fu">readRDS</span>(</span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="st">&quot;results&quot;</span>, <span class="st">&quot;real_data&quot;</span>, <span class="st">&quot;zeisel-seurat_wilcox.rds&quot;</span>)</span>
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb8-5"><a href="#cb8-5" aria-hidden="true" tabindex="-1"></a>top_mgs <span class="ot">&lt;-</span> seurat_wilcox<span class="sc">$</span>result <span class="sc">%&gt;%</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">&quot;oligodendrocytes&quot;</span>) <span class="sc">%&gt;%</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">%&gt;%</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">&lt;-</span> <span class="fu">plotExpression</span>(zeisel, <span class="at">x =</span> <span class="st">&quot;label&quot;</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>
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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">&quot;figures&quot;</span>, <span class="st">&quot;final&quot;</span>, <span class="st">&quot;seurat-wilcox-top-oligodencrocytes.pdf&quot;</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">&quot;in&quot;</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">&lt;-</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">&quot;results&quot;</span>, <span class="st">&quot;real_data&quot;</span>, <span class="st">&quot;zeisel-seurat_t.rds&quot;</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">%&gt;%</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">&quot;interneurons&quot;</span>) <span class="sc">%&gt;%</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
      &lt;dbl&gt;       &lt;dbl&gt; &lt;fct&gt;         &lt;dbl&gt; &lt;chr&gt;         &lt;dbl&gt;            &lt;dbl&gt;
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">&lt;-</span> <span class="fu">plotExpression</span>(zeisel, <span class="at">x =</span> <span class="st">&quot;label&quot;</span>, <span class="fu">c</span>(<span class="st">&quot;Snap25&quot;</span>, <span class="st">&quot;Ndrg4&quot;</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>
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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/not-found-seurat-t-interneurons-markers-1.svg" target="_blank">8b989e1</a>
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Jeffrey Pullin
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2022-05-02
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<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">&lt;-</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">&quot;results&quot;</span>, <span class="st">&quot;real_data&quot;</span>, <span class="st">&quot;zeisel-scran_t_any.rds&quot;</span>)</span>
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a>)</span>