Skip to content

Commit

Permalink
Deployed 7bb9e56 with MkDocs version: 1.1.2
Browse files Browse the repository at this point in the history
  • Loading branch information
@taniawyss
taniawyss committed Mar 5, 2024
1 parent 25387c2 commit 0d4a674
Show file tree
Hide file tree
Showing 13 changed files with 109 additions and 17 deletions.
Binary file added assets/images/barplot1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added assets/images/barplot2.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added assets/images/cnetplot1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added assets/images/enrichplot1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added assets/images/lollipop.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added assets/images/ridgeplot1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added assets/pdf/DEG_pvalue_corr_intro_video_slides.pdf
View file
Binary file not shown.
76 changes: 71 additions & 5 deletions bonus_code/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -297,8 +297,15 @@
</li>

<li class="md-nav__item">
<a href="#code-for-a-heatmap-of-p-values" class="md-nav__link">
Code for a heatmap of p-values
<a href="#code-for-a-heatmap-of-p-values-with-ggplot2" class="md-nav__link">
Code for a heatmap of p-values with ggplot2
</a>

</li>

<li class="md-nav__item">
<a href="#code-for-a-lollipop-plot-with-ggplot2" class="md-nav__link">
Code for a lollipop plot with ggplot2
</a>

</li>
Expand Down Expand Up @@ -392,8 +399,15 @@
</li>

<li class="md-nav__item">
<a href="#code-for-a-heatmap-of-p-values" class="md-nav__link">
Code for a heatmap of p-values
<a href="#code-for-a-heatmap-of-p-values-with-ggplot2" class="md-nav__link">
Code for a heatmap of p-values with ggplot2
</a>

</li>

<li class="md-nav__item">
<a href="#code-for-a-lollipop-plot-with-ggplot2" class="md-nav__link">
Code for a lollipop plot with ggplot2
</a>

</li>
Expand Down Expand Up @@ -561,7 +575,7 @@ <h2 id="code-for-barplots-with-ggplot2">Code for barplots with ggplot2</h2>
<img src="../assets/images/barplot_NES.png" width="300"/>
</figure>
</p>
<h2 id="code-for-a-heatmap-of-p-values">Code for a heatmap of p-values</h2>
<h2 id="code-for-a-heatmap-of-p-values-with-ggplot2">Code for a heatmap of p-values with ggplot2</h2>
<p>For heatmaps, ggplot2 can also be used. Here is an example for a heatmap of the p-values of 6 different gene sets (gs), and the
p-value for each gene set was calculated in two comparisons, so we compared the enrichment in genes differentially expressed
between NK cells and Th cells, and between NK cells and CD8 T cells (note that this is a dummy example just to show you the
Expand Down Expand Up @@ -628,6 +642,58 @@ <h2 id="code-for-a-heatmap-of-p-values">Code for a heatmap of p-values</h2>
<img src="../assets/images/heatmap_p_value_ORA.png" width="300"/>
</figure>

<h2 id="code-for-a-lollipop-plot-with-ggplot2">Code for a lollipop plot with ggplot2</h2>
<p>In this lollipop of GSEA results of leukocyte-related GO pathways, the color will represent up- (red) or down-regulated (blue) gene sets, the dot size represents the setSize. The length of the gene set description is truncated to 50 characters. We use the GSEA results that we obtained after selecting the leukocyte-related GO pathways at the end of exercise 3</p>
<div class="highlight"><pre><span></span><code><span class="c1"># Bonus: lollipop plot of p-values of leukocyte-related GO pathways. The </span>
<span class="c1"># color will represent up- (red) or down-regulated (blue) gene sets, </span>
<span class="c1"># the dot size represents the setSize.</span>
<span class="c1"># The length of the gene set description is truncated to 50 characters:</span>

<span class="c1"># We use the GSEA results that we obtained after selecting the leukocyte-related GO pathways at the end of exercise 3</span>
<span class="n">df</span> <span class="o">&lt;-</span> <span class="n">GO_NK_Th_selection</span><span class="o">@</span><span class="n">result</span>
<span class="nf">head</span><span class="p">(</span><span class="n">df</span><span class="p">[,</span><span class="m">1</span><span class="o">:</span><span class="m">8</span><span class="p">])</span>
<span class="c1"># ID Description setSize enrichmentScore NES pvalue p.adjust qvalue</span>
<span class="c1"># GO:0097529 GO:0097529 myeloid leukocyte migration 182 0.3358543 1.459329 0.0060333962 0.04957978 0.03849908</span>
<span class="c1"># GO:0030595 GO:0030595 leukocyte chemotaxis 186 0.3314487 1.446607 0.0057064461 0.04766950 0.03701573</span>
<span class="c1"># GO:0007159 GO:0007159 leukocyte cell-cell adhesion 335 0.2955485 1.381506 0.0037782543 0.03815146 0.02962490</span>
<span class="c1"># GO:0001776 GO:0001776 leukocyte homeostasis 99 -0.3891370 -1.552210 0.0037570540 0.03812616 0.02960525</span>
<span class="c1"># GO:0002685 GO:0002685 regulation of leukocyte migration 185 0.3418586 1.489716 0.0020160142 0.02593948 0.02014220</span>
<span class="c1"># GO:0070661 GO:0070661 leukocyte proliferation 273 0.3247110 1.493837 0.0009132421 0.01545176 0.01199841</span>

<span class="n">df</span><span class="o">$</span><span class="n">mycolor</span> <span class="o">&lt;-</span> <span class="nf">ifelse</span><span class="p">(</span><span class="n">df</span><span class="o">$</span><span class="n">NES</span><span class="o">&lt;</span><span class="m">0</span><span class="p">,</span> <span class="s">&quot;cornflowerblue&quot;</span><span class="p">,</span><span class="s">&quot;indianred2&quot;</span><span class="p">)</span>

<span class="n">df</span> <span class="o">&lt;-</span> <span class="n">df</span><span class="p">[</span><span class="nf">order</span><span class="p">(</span><span class="n">df</span><span class="o">$</span><span class="n">pvalue</span><span class="p">,</span> <span class="n">decreasing</span> <span class="o">=</span> <span class="bp">T</span><span class="p">),]</span> <span class="c1">#revert the order of the rows</span>
<span class="n">df</span><span class="o">$</span><span class="n">Label</span> <span class="o">&lt;-</span><span class="n">stringr</span><span class="o">::</span><span class="nf">str_trunc</span><span class="p">(</span><span class="n">df</span><span class="o">$</span><span class="n">Description</span><span class="p">,</span> <span class="m">50</span><span class="p">,</span> <span class="s">&quot;right&quot;</span><span class="p">)</span> <span class="c1"># keep max 50 character in a string (nchar(&quot;string&quot;) to count characters)</span>
<span class="n">df</span><span class="o">$</span><span class="n">Label</span> <span class="o">&lt;-</span> <span class="nf">factor</span><span class="p">(</span><span class="n">df</span><span class="o">$</span><span class="n">Label</span><span class="p">,</span> <span class="n">levels</span> <span class="o">=</span> <span class="nf">c</span><span class="p">(</span><span class="n">df</span><span class="o">$</span><span class="n">Label</span><span class="p">))</span>

<span class="c1"># Use limits of the x-axis range according to the range of p.values:</span>
<span class="n">max_x</span> <span class="o">&lt;-</span> <span class="nf">round</span><span class="p">(</span><span class="nf">max</span><span class="p">(</span><span class="o">-</span><span class="nf">log10</span><span class="p">(</span><span class="n">df</span><span class="o">$</span><span class="n">p.adjust</span><span class="p">)),</span> <span class="n">digits</span> <span class="o">=</span> <span class="m">0</span><span class="p">)</span> <span class="o">+</span> <span class="m">0.5</span>
<span class="n">xlimits</span> <span class="o">&lt;-</span> <span class="nf">c</span><span class="p">(</span><span class="m">0</span><span class="p">,</span> <span class="n">max_x</span><span class="p">)</span>
<span class="n">xbreaks</span> <span class="o">&lt;-</span> <span class="nf">seq_along</span><span class="p">(</span><span class="m">0</span><span class="o">:</span><span class="n">max_x</span><span class="p">)</span>

<span class="c1"># Create the plot:</span>
<span class="n">p</span> <span class="o">&lt;-</span> <span class="nf">ggplot</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="nf">aes</span><span class="p">(</span><span class="n">x</span> <span class="o">=</span> <span class="n">Label</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="o">-</span><span class="nf">log10</span><span class="p">(</span><span class="n">p.adjust</span><span class="p">),</span> <span class="n">fill</span> <span class="o">=</span> <span class="n">mycolor</span><span class="p">))</span> <span class="o">+</span>
<span class="nf">geom_segment</span><span class="p">(</span><span class="nf">aes</span><span class="p">(</span><span class="n">x</span> <span class="o">=</span> <span class="n">Label</span><span class="p">,</span> <span class="n">xend</span> <span class="o">=</span> <span class="n">Label</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="m">0</span><span class="p">,</span> <span class="n">yend</span> <span class="o">=</span> <span class="o">-</span><span class="nf">log10</span><span class="p">(</span><span class="n">p.adjust</span><span class="p">)),</span>
<span class="n">color</span> <span class="o">=</span> <span class="n">df</span><span class="o">$</span><span class="n">mycolor</span><span class="p">,</span> <span class="n">lwd</span> <span class="o">=</span> <span class="m">1</span><span class="p">)</span> <span class="o">+</span>
<span class="nf">geom_point</span><span class="p">(</span><span class="n">pch</span> <span class="o">=</span> <span class="m">21</span><span class="p">,</span> <span class="n">bg</span> <span class="o">=</span> <span class="n">df</span><span class="o">$</span><span class="n">mycolor</span><span class="p">,</span> <span class="nf">aes</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="n">df</span><span class="o">$</span><span class="n">setSize</span><span class="p">),</span> <span class="n">color</span><span class="o">=</span><span class="n">df</span><span class="o">$</span><span class="n">mycolor</span><span class="p">)</span> <span class="o">+</span>
<span class="nf">scale_size</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s">&quot;Number\nof genes&quot;</span><span class="p">)</span> <span class="o">+</span>
<span class="nf">scale_y_continuous</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="nf">expression</span><span class="p">(</span><span class="s">&quot;-&quot;</span><span class="o">*</span><span class="s">&quot;log&quot;</span><span class="p">[</span><span class="m">10</span><span class="p">]</span><span class="o">*</span><span class="s">&quot;(p-value)&quot;</span><span class="p">),</span>
<span class="n">limits</span><span class="o">=</span><span class="n">xlimits</span><span class="p">,</span>
<span class="n">breaks</span><span class="o">=</span><span class="n">xbreaks</span><span class="p">)</span> <span class="o">+</span>
<span class="nf">scale_x_discrete</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s">&quot;&quot;</span><span class="p">)</span> <span class="o">+</span>
<span class="nf">theme_bw</span><span class="p">(</span><span class="n">base_size</span><span class="o">=</span><span class="m">10</span><span class="p">,</span> <span class="n">base_family</span> <span class="o">=</span> <span class="s">&quot;Helvetica&quot;</span><span class="p">)</span> <span class="o">+</span>
<span class="nf">theme</span><span class="p">(</span><span class="n">axis.text</span><span class="o">=</span><span class="nf">element_text</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="m">12</span><span class="p">,</span> <span class="n">colour</span> <span class="o">=</span> <span class="s">&quot;black&quot;</span><span class="p">),</span>
<span class="n">axis.title</span><span class="o">=</span><span class="nf">element_text</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="m">14</span><span class="p">))</span> <span class="o">+</span>
<span class="nf">ggtitle</span><span class="p">(</span><span class="s">&quot;Leukocyte-related GO pathways&quot;</span><span class="p">)</span> <span class="o">+</span>
<span class="nf">coord_flip</span><span class="p">()</span>

<span class="n">p</span>
</code></pre></div>
<p>You will obtain the following lollipop plot :</p>
<figure>
<img src="../assets/images/lollipop.png" width="700"/>
</figure>

<h2 id="small-information-on-a-typical-rnaseq-workflow">Small information on a typical RNAseq workflow</h2>
<p><a class="md-button" href="../assets/pdf/brief_RNAseq_workflow.pdf">Download pdf</a></p>
<h2 id="example-for-de-analysis-with-deseq2">Example for DE analysis with DESeq2</h2>
Expand Down
Loading

0 comments on commit 0d4a674

Please sign in to comment.