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docs/articles/consensus_wgcna.html

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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">

<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">

<script src="../pkgdown.js"></script><meta property="og:title" content="Consensus network analysis">

<meta property="og:description" content="Tutorial for applying the core functions of scWGCNA.

<meta property="og:description" content="Tutorial for performing consensus co-expression network analysis.

">

<meta property="og:image" content="https://smorabit.github.io/scWGCNA/logo.png">

<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -137,8 +137,58 @@ 


    

    

<p>Load the snRNA-seq data and the required libraries:</p>

<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">'hello world'</span><span class="op">)</span></code></pre></div>

<code class="sourceCode R"><span class="co"># single-cell analysis package</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://satijalab.org/seurat" class="external-link">Seurat</a></span><span class="op">)</span>



<span class="co"># plotting and data science packages</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidyverse.tidyverse.org" class="external-link">tidyverse</a></span><span class="op">)</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://wilkelab.org/cowplot/" class="external-link">cowplot</a></span><span class="op">)</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://patchwork.data-imaginist.com" class="external-link">patchwork</a></span><span class="op">)</span>



<span class="co"># co-expression network analysis packages:</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="http://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/" class="external-link">WGCNA</a></span><span class="op">)</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://smorabit.github.io/scWGCNA/">scWGCNA</a></span><span class="op">)</span>



<span class="co"># network analysis &amp; visualization package:</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://igraph.org" class="external-link">igraph</a></span><span class="op">)</span>



<span class="co"># using the cowplot theme for ggplot</span>

<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme_get.html" class="external-link">theme_set</a></span><span class="op">(</span><span class="fu"><a href="https://wilkelab.org/cowplot/reference/theme_cowplot.html" class="external-link">theme_cowplot</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>



<span class="co"># set random seed for reproducibility</span>

<span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">12345</span><span class="op">)</span>



<span class="co"># load the Zhou et al snRNA-seq dataset</span>

<span class="va">seurat_ref</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">'data/Zhou_control.rds'</span><span class="op">)</span></code></pre></div>

<p>Setup data:</p>

<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="co"># just run SetMultiExpr by itself</span>

<span class="va">seurat_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/SetMultiExpr.html">SetMultiExpr</a></span><span class="op">(</span>

  <span class="va">seurat_obj</span>,

  group_name <span class="op">=</span> <span class="st">"INH"</span>,

  group.by <span class="op">=</span> <span class="st">"cell_type"</span>,

  multi.group.by <span class="op">=</span> <span class="st">"Sex"</span>,

  multi_groups <span class="op">=</span> <span class="cn">NULL</span>

<span class="op">)</span></code></pre></div>

<p>Run the consensus network</p>

<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="va">seurat_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ConstructNetwork.html">ConstructNetwork</a></span><span class="op">(</span>

  <span class="va">seurat_obj</span>,

  soft_power<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">5</span>,<span class="fl">8</span><span class="op">)</span>, <span class="co"># soft power can be a single number of a vector with a value for each datExpr in multiExpr</span>

  consensus<span class="op">=</span><span class="cn">TRUE</span>

<span class="op">)</span></code></pre></div>

<p>MEs</p>

<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="co"># compute all MEs in the full single-cell 21  dataset</span>

<span class="va">seurat_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ModuleEigengenes.html">ModuleEigengenes</a></span><span class="op">(</span>

  <span class="va">seurat_obj</span>,

  group.by.vars<span class="op">=</span><span class="st">"Sample"</span>

<span class="op">)</span>



<span class="co"># compute module connectivity:</span>

<span class="va">seurat_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ModuleConnectivity.html">ModuleConnectivity</a></span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">)</span></code></pre></div>

  </div>



  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">

docs/articles/figures/projection/mouse_preservation_all.png

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docs/articles/figures/projection/mouse_preservation_summary.png

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docs/articles/index.html

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      <dl><dt><a href="basic_tutorial.html">scWGCNA Basics</a></dt>

        <dd><p>Tutorial for applying the core functions of scWGCNA.</p>

        </dd><dt><a href="consensus_wgcna.html">Consensus network analysis</a></dt>

        <dd><p>Tutorial for applying the core functions of scWGCNA.</p>

        <dd><p>Tutorial for performing consensus co-expression network analysis.</p>

        </dd><dt><a href="customization.html">Module customization</a></dt>

        <dd><p>Tutorial for customizing module colors and module names in scWGCNA.</p>

        </dd><dt><a href="enrichment_analysis.html">Enrichment analysis</a></dt>

docs/articles/module_trait_correlation.html

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<p>Load the snRNA-seq data and the required libraries:</p>

<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">'hello world'</span><span class="op">)</span></code></pre></div>

<code class="sourceCode R"><span class="co"># single-cell analysis package</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://satijalab.org/seurat" class="external-link">Seurat</a></span><span class="op">)</span>



<span class="co"># plotting and data science packages</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidyverse.tidyverse.org" class="external-link">tidyverse</a></span><span class="op">)</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://wilkelab.org/cowplot/" class="external-link">cowplot</a></span><span class="op">)</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://patchwork.data-imaginist.com" class="external-link">patchwork</a></span><span class="op">)</span>



<span class="co"># co-expression network analysis packages:</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="http://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/" class="external-link">WGCNA</a></span><span class="op">)</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://smorabit.github.io/scWGCNA/">scWGCNA</a></span><span class="op">)</span>



<span class="co"># network analysis &amp; visualization package:</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://igraph.org" class="external-link">igraph</a></span><span class="op">)</span>



<span class="co"># packages for TF motif analysis</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">JASPAR2020</span><span class="op">)</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">motifmatchr</span><span class="op">)</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">TFBSTools</span><span class="op">)</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">EnsDb.Hsapiens.v86</span><span class="op">)</span>

<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">GenomicRanges</span><span class="op">)</span>



<span class="co"># using the cowplot theme for ggplot</span>

<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/theme_get.html" class="external-link">theme_set</a></span><span class="op">(</span><span class="fu"><a href="https://wilkelab.org/cowplot/reference/theme_cowplot.html" class="external-link">theme_cowplot</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>



<span class="co"># set random seed for reproducibility</span>

<span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">12345</span><span class="op">)</span>



<span class="co"># load the Zhou et al snRNA-seq dataset</span>

<span class="va">seurat_ref</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">'data/Zhou_control.rds'</span><span class="op">)</span></code></pre></div>

<p>Compute module trait correlation split by cell type:</p>

<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="va">seurat_obj</span><span class="op">$</span><span class="va">Sample</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/character.html" class="external-link">as.character</a></span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">$</span><span class="va">Sample</span><span class="op">)</span>, levels<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/unique.html" class="external-link">unique</a></span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">$</span><span class="va">Sample</span><span class="op">)</span><span class="op">)</span>

<span class="va">seurat_obj</span><span class="op">$</span><span class="va">msex</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">$</span><span class="va">msex</span><span class="op">)</span>

<span class="va">seurat_obj</span><span class="op">$</span><span class="va">age_death</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">as.numeric</a></span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">$</span><span class="va">age_death</span><span class="op">)</span>



<span class="va">cur_traits</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'Sample'</span>, <span class="st">'total_counts_mt'</span>, <span class="st">'n_genes_by_counts'</span>, <span class="st">'age_death'</span>, <span class="st">'braaksc'</span>, <span class="st">'msex'</span><span class="op">)</span>

<span class="va">data_types</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">cur_traits</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">{</span><span class="fu"><a href="https://rdrr.io/r/base/class.html" class="external-link">class</a></span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">@</span><span class="va">meta.data</span><span class="op">[</span>,<span class="va">x</span><span class="op">]</span><span class="op">)</span><span class="op">}</span><span class="op">)</span>



<span class="va">cur_traits</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">'braaksc'</span>, <span class="st">'pmi'</span>, <span class="st">'msex'</span><span class="op">)</span>



<span class="va">seurat_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/ModuleTraitCorrelation.html">ModuleTraitCorrelation</a></span><span class="op">(</span>

  <span class="va">seurat_obj</span>,

  traits <span class="op">=</span> <span class="va">cur_traits</span>,

  group.by<span class="op">=</span><span class="st">'cell_type'</span>

<span class="op">)</span>



<span class="va">temp</span> <span class="op">&lt;-</span> <span class="fu">GetModuleTraitCorrelation</span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">)</span>

<span class="va">cor_list</span> <span class="op">&lt;-</span> <span class="va">temp</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>

<span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">cor_list</span><span class="op">)</span></code></pre></div>

<p>Plot the results as a heatmap for each cell type:</p>

<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="va">plot_list</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span>

<span class="kw">for</span><span class="op">(</span><span class="va">i</span> <span class="kw">in</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">cor_list</span><span class="op">)</span><span class="op">)</span><span class="op">{</span>

  <span class="va">cor_mat</span> <span class="op">&lt;-</span> <span class="va">cor_list</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span>

  <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span>



  <span class="va">plot_df</span> <span class="op">&lt;-</span> <span class="fu">reshape2</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/reshape2/man/melt.html" class="external-link">melt</a></span><span class="op">(</span><span class="va">cor_mat</span><span class="op">)</span>

  <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">plot_df</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Trait"</span>, <span class="st">"Module"</span>, <span class="st">"cor"</span><span class="op">)</span>



  <span class="va">plot_list</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">plot_df</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x<span class="op">=</span><span class="va">Module</span>, y<span class="op">=</span><span class="va">Trait</span>, fill<span class="op">=</span><span class="va">cor</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span>

    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_tile.html" class="external-link">geom_tile</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span>

    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_gradient.html" class="external-link">scale_fill_gradient2</a></span><span class="op">(</span>limits<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">1</span>,<span class="fl">1</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span>

    <span class="fu"><a href="https://satijalab.org/seurat/reference/SeuratTheme.html" class="external-link">RotatedAxis</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ylab</a></span><span class="op">(</span><span class="st">''</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">xlab</a></span><span class="op">(</span><span class="st">''</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span>



<span class="op">}</span></code></pre></div>

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