Commit 8337a343 authored by smorabit's avatar smorabit
Browse files

added note about grey modules into basics tutorial

parent a2f7e828

docs/articles/basic_tutorial.html

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@@ -331,6 +331,7 @@ Output 
  setDatExpr<span class="op">=</span><span class="cn">FALSE</span>

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

<p>hdWGCNA also includes a function <code>PlotDendrogram</code> to visualize the WGCNA dendrogram, a common visualization to show the different co-expression modules resulting from the network analysis. Each leaf on the dendrogram represents a single gene, and the color at the bottom indicates the co-expression module assignment.</p>

<p><strong>Importantly, the “grey” module consists of genes that were not grouped into any co-expression module. The grey module should be ignored for all downstream analysis and interpretation.</strong></p>

<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="fu"><a href="../reference/PlotDendrogram.html">PlotDendrogram</a></span><span class="op">(</span><span class="va">seurat_obj</span>, main<span class="op">=</span><span class="st">'INH hdWGCNA Dendrogram'</span><span class="op">)</span></code></pre></div>

<p><img src="figures/basic_tutorial/inh_dendro.png" width="600" height="600"></p>

docs/articles/motif_analysis.html

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@@ -160,7 +160,7 @@ 
<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="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://bioconductor.org/packages/GenomicRanges" class="external-link">GenomicRanges</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>
@@ -192,7 +192,7 @@ 
<span class="va">target_genes</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/GetMotifTargets.html">GetMotifTargets</a></span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">)</span>



<span class="co"># check target genes for one TF:</span>

<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">target_genes</span><span class="op">$</span><span class="va">SOX9</span><span class="op">)</span></code></pre></div>

<span class="fu"><a href="https://rdrr.io/pkg/S4Vectors/man/Vector-class.html" class="external-link">head</a></span><span class="op">(</span><span class="va">target_genes</span><span class="op">$</span><span class="va">SOX9</span><span class="op">)</span></code></pre></div>

<details><summary>

Output

</summary><pre><code>[1] "OR4F5"  "TTLL10" "SDF4"   "ATAD3C" "MIB2"   "CDK11B"</code></pre>
@@ -202,7 +202,7 @@ Output 
<span class="va">seurat_obj</span><span class="op">&lt;-</span> <span class="fu"><a href="../reference/OverlapModulesMotifs.html">OverlapModulesMotifs</a></span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">)</span>



<span class="co"># look at the overlap data</span>

<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu"><a href="../reference/GetMotifOverlap.html">GetMotifOverlap</a></span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">)</span><span class="op">)</span></code></pre></div>

<span class="fu"><a href="https://rdrr.io/pkg/S4Vectors/man/Vector-class.html" class="external-link">head</a></span><span class="op">(</span><span class="fu"><a href="../reference/GetMotifOverlap.html">GetMotifOverlap</a></span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">)</span><span class="op">)</span></code></pre></div>

<details><summary>

Output

</summary><pre><code>module           tf      color odds_ratio       pval        fdr
@@ -226,7 +226,7 @@ FOXD1 0.001482800 5</code></pre> 
  <span class="va">seurat_obj</span>,

  <span class="co">#motif_font = 'xkcd_regular',</span>

  outdir <span class="op">=</span> <span class="st">'motifs/MotifOverlaps/'</span>,

  plot_size<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">6</span><span class="op">)</span>

  plot_size<span class="op">=</span><span class="fu"><a href="https://rdrr.io/pkg/S4Vectors/man/Vector-class.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">5</span>,<span class="fl">6</span><span class="op">)</span>

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

<p><img src="figures/motif_analysis/motif_barplot.png" width="500" height="500"></p>

<p>Compute motif target gene expression score:</p>
@@ -240,7 +240,7 @@ FOXD1 0.001482800 5</code></pre> 
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">

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



<span class="va">cur_df</span> <span class="op">&lt;-</span> <span class="va">df</span> <span class="op"><a href="https://rdrr.io/pkg/igraph/man/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">tf</span> <span class="op">==</span> <span class="st">'SOX9'</span><span class="op">)</span>

<span class="va">cur_df</span> <span class="op">&lt;-</span> <span class="va">df</span> <span class="op"><a href="https://rdrr.io/pkg/igraph/man/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/BiocGenerics/man/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">tf</span> <span class="op">==</span> <span class="st">'SOX9'</span><span class="op">)</span>



<span class="va">plot_var</span> <span class="op">&lt;-</span> <span class="st">'odds_ratio'</span>

<span class="va">p</span> <span class="op">&lt;-</span> <span class="va">cur_df</span> <span class="op"><a href="https://rdrr.io/pkg/igraph/man/pipe.html" class="external-link">%&gt;%</a></span>

docs/articles/network_visualizations.html

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@@ -256,7 +256,7 @@ 
Code

</summary><div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="co"># different label weights to test</span>

<span class="va">n_hubs</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="fl">1</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">*</span><span class="fl">5</span><span class="op">)</span>

<span class="va">n_hubs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/S4Vectors/man/Vector-class.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">*</span><span class="fl">5</span><span class="op">)</span>



<span class="co"># loop through different weights</span>

<span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span><span class="op">)</span>
@@ -274,7 +274,7 @@ Code 
  <span class="co"># add to ongoing dataframe</span>

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

  <span class="va">cur_df</span><span class="op">$</span><span class="va">n_hubs</span> <span class="op">&lt;-</span> <span class="va">cur_hubs</span>

  <span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">df</span>, <span class="va">cur_df</span><span class="op">)</span>

  <span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/BiocGenerics/man/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">df</span>, <span class="va">cur_df</span><span class="op">)</span>

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



<span class="co"># ggplot animation library</span>
@@ -350,7 +350,7 @@ Code 
  <span class="co"># add to ongoing dataframe</span>

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

  <span class="va">cur_df</span><span class="op">$</span><span class="va">weight</span> <span class="op">&lt;-</span> <span class="va">cur_weight</span>

  <span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">df</span>, <span class="va">cur_df</span><span class="op">)</span>

  <span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/BiocGenerics/man/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">df</span>, <span class="va">cur_df</span><span class="op">)</span>

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



<span class="co"># ggplot animation library</span>

docs/articles/projecting_modules.html

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@@ -244,7 +244,7 @@ Code 
<span class="va">projected_hMEs</span> <span class="op">&lt;-</span>  <span class="fu"><a href="../reference/GetMEs.html">GetMEs</a></span><span class="op">(</span><span class="va">seurat_query</span>, harmonized<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span>



<span class="co"># add hMEs to Seurat meta-data:</span>

<span class="va">seurat_query</span><span class="op">@</span><span class="va">meta.data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">cbind</a></span><span class="op">(</span>

<span class="va">seurat_query</span><span class="op">@</span><span class="va">meta.data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/BiocGenerics/man/cbind.html" class="external-link">cbind</a></span><span class="op">(</span>

  <span class="va">seurat_query</span><span class="op">@</span><span class="va">meta.data</span>,

  <span class="va">projected_hMEs</span>

<span class="op">)</span>
@@ -252,7 +252,7 @@ Code 
<span class="co"># plot with Seurat's DotPlot function</span>

<span class="va">p</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://satijalab.org/seurat/reference/DotPlot.html" class="external-link">DotPlot</a></span><span class="op">(</span>

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

    features <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">projected_hMEs</span><span class="op">)</span>,

    features <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/BiocGenerics/man/row_colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">projected_hMEs</span><span class="op">)</span>,

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

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

docs/articles/projecting_modules_cross.html

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