Commit d4a12a1a authored by smorabit's avatar smorabit
Browse files

update to mt correlation vignette

parent d29ee1b5

R/plotting.R

+2 −2
Original line number Diff line number Diff line
@@ -1781,7 +1781,8 @@ PlotModuleTraitCorrelation <- function( 
        axis.line=element_blank(),

        axis.ticks.y=element_blank(),

        axis.text.y.left = element_blank(),

        legend.title = element_blank()

        legend.title = element_blank(),

        legend.position='bottom'

      )



    if(!is.null(label)){
@@ -1820,7 +1821,6 @@ PlotModuleTraitCorrelation <- function( 
        heights = c(rep(1, length(plot_list)-1), 0.15)

      ) +

      plot_annotation(

        title='Module Trait Correlation',

        theme=theme(

          plot.title=element_text(hjust=0.5),

          legend.position = 'bottom',

README.md

+1 −1
Original line number Diff line number Diff line
@@ -46,7 +46,7 @@ install.packages(c("Seurat", "WGCNA", "igraph", "devtools")) 


```



Now you can install the scWGCNA package using `devtools`. We are planning to add scWGCNA to CRAN and Bioconductor upon the 1.0 release in the next couple of months.

Now you can install the scWGCNA package using `devtools`.



```r

devtools::install_github('smorabit/scWGCNA', branch='dev')

docs/articles/figures/mt_correlation/ME_Trait_correlation_fdr.png

0 → 100644
+717 KiB
Loading image diff...

docs/articles/module_trait_correlation.html

+17 −33
Original line number Diff line number Diff line
@@ -151,22 +151,9 @@ 
<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>
@@ -178,33 +165,30 @@ 
<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="co"># list of traits</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="st">'age_death'</span>, <span class="st">'doublet_scores'</span>, <span class="st">'nCount_RNA'</span>, <span class="st">'nFeature_RNA'</span>, <span class="st">'total_counts_mt'</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>

<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>

<code class="sourceCode R"><span class="fu">PlotModuleTraitCorrelation</span><span class="op">(</span>

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

  label <span class="op">=</span> <span class="st">'fdr'</span>,

  label_symbol <span class="op">=</span> <span class="st">'stars'</span>,

  text_size <span class="op">=</span> <span class="fl">2</span>,

  text_digits <span class="op">=</span> <span class="fl">2</span>,

  text_color <span class="op">=</span> <span class="st">'white'</span>,

  high_color <span class="op">=</span> <span class="st">'yellow'</span>,

  mid_color <span class="op">=</span> <span class="st">'black'</span>,

  low_color <span class="op">=</span> <span class="st">'purple'</span>,

  plot_max <span class="op">=</span> <span class="fl">0.2</span>,

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

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

<p><img src="figures/mt_correlation/ME_Trait_correlation_fdr.png" width="600" height="600"></p>

  </div>



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

docs/articles/motif_analysis.html

+4 −3
Original line number Diff line number Diff line
@@ -182,7 +182,7 @@ 
  <span class="va">seurat_obj</span>,

  species_genome <span class="op">=</span> <span class="st">'hg38'</span>,

  pfm <span class="op">=</span> <span class="va">pfm_core</span>,

  EnsDb <span class="op">=</span> <span class="va">EnsDb.Hsapeins.v86</span>

  EnsDb <span class="op">=</span> <span class="va">EnsDb.Hsapiens.v86</span>

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

<span class="fu"><a href="https://rdrr.io/r/base/dim.html" class="external-link">dim</a></span><span class="op">(</span><span class="fu">GetMotifMatrix</span><span class="op">(</span><span class="va">seurat_obj</span><span class="op">)</span><span class="op">)</span>
@@ -200,12 +200,13 @@ 
<span class="fu"><a href="../reference/MotifOverlapBarPlot.html">MotifOverlapBarPlot</a></span><span class="op">(</span>

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

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

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

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

<p>Compute motif target gene expression score:</p>

<div class="sourceCode" id="cb4"><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/MotifTargetScore.html">MotifTargetScore</a></span><span class="op">(</span>

<code class="sourceCode R"><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">UCell</span><span class="op">)</span>

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

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

  method<span class="op">=</span><span class="st">'UCell'</span>

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

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