Updated contents at 20240314-002819

NBISweden · Mar 13, 2024 · b7d625b · b7d625b
1 parent 40b5c9a
commit b7d625b
Show file tree

Hide file tree

Showing 303 changed files with 1,068,106 additions and 19 deletions.
diff --git a/2403-canvas/data/GO_ORA_results.png b/2403-canvas/data/GO_ORA_results.png
diff --git a/2403-canvas/index.html b/2403-canvas/index.html
@@ -201,7 +201,7 @@ <h1>Analysis of RNA-Seq Data</h1>
 <hr />
 <div class="landing-update">
 <p class="small" style="color:#bdbdbd;">
-Last updated on <svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#bdbdbd;overflow:visible;position:relative;"><path d="M152 24c0-13.3-10.7-24-24-24s-24 10.7-24 24V64H64C28.7 64 0 92.7 0 128v16 48V448c0 35.3 28.7 64 64 64H384c35.3 0 64-28.7 64-64V192 144 128c0-35.3-28.7-64-64-64H344V24c0-13.3-10.7-24-24-24s-24 10.7-24 24V64H152V24zM48 192h80v56H48V192zm0 104h80v64H48V296zm128 0h96v64H176V296zm144 0h80v64H320V296zm80-48H320V192h80v56zm0 160v40c0 8.8-7.2 16-16 16H320V408h80zm-128 0v56H176V408h96zm-144 0v56H64c-8.8 0-16-7.2-16-16V408h80zM272 248H176V192h96v56z"/></svg> 13-Mar-2024 at <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#bdbdbd;overflow:visible;position:relative;"><path d="M464 256A208 208 0 1 1 48 256a208 208 0 1 1 416 0zM0 256a256 256 0 1 0 512 0A256 256 0 1 0 0 256zM232 120V256c0 8 4 15.5 10.7 20l96 64c11 7.4 25.9 4.4 33.3-6.7s4.4-25.9-6.7-33.3L280 243.2V120c0-13.3-10.7-24-24-24s-24 10.7-24 24z"/></svg> 10:32:09 PM .
+Last updated on <svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#bdbdbd;overflow:visible;position:relative;"><path d="M152 24c0-13.3-10.7-24-24-24s-24 10.7-24 24V64H64C28.7 64 0 92.7 0 128v16 48V448c0 35.3 28.7 64 64 64H384c35.3 0 64-28.7 64-64V192 144 128c0-35.3-28.7-64-64-64H344V24c0-13.3-10.7-24-24-24s-24 10.7-24 24V64H152V24zM48 192h80v56H48V192zm0 104h80v64H48V296zm128 0h96v64H176V296zm144 0h80v64H320V296zm80-48H320V192h80v56zm0 160v40c0 8.8-7.2 16-16 16H320V408h80zm-128 0v56H176V408h96zm-144 0v56H64c-8.8 0-16-7.2-16-16V408h80zM272 248H176V192h96v56z"/></svg> 13-Mar-2024 at <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#bdbdbd;overflow:visible;position:relative;"><path d="M464 256A208 208 0 1 1 48 256a208 208 0 1 1 416 0zM0 256a256 256 0 1 0 512 0A256 256 0 1 0 0 256zM232 120V256c0 8 4 15.5 10.7 20l96 64c11 7.4 25.9 4.4 33.3-6.7s4.4-25.9-6.7-33.3L280 243.2V120c0-13.3-10.7-24-24-24s-24 10.7-24 24z"/></svg> 11:25:45 PM .
 </p>
 </div>
 </div>

diff --git a/2403-canvas/lab_dge_files/figure-html/unnamed-chunk-27-1.png b/2403-canvas/lab_dge_files/figure-html/unnamed-chunk-27-1.png
diff --git a/2403-canvas/lab_dge_files/figure-html/unnamed-chunk-27-2.png b/2403-canvas/lab_dge_files/figure-html/unnamed-chunk-27-2.png
diff --git a/2403-canvas/lab_eda_files/figure-html/unnamed-chunk-18-1.png b/2403-canvas/lab_eda_files/figure-html/unnamed-chunk-18-1.png
diff --git a/2403-canvas/lab_functional.html b/2403-canvas/lab_functional.html
@@ -488,7 +488,7 @@ <h2><span class="header-section-number">2.2</span> GSEA</h2>
 # Load hallmark pathways
 hallmark_pathways &lt;- gmtPathways(&quot;data/MSigDB_files/h.all.v6.2.symbols.gmt.txt&quot;)</code></pre>
 </div>
-<p>Once our list of genes are sorted (from highest to lowest expression in day 7), we can proceed with the enrichment itself. Here, we will be using the <code>fgsea()</code> function. This will result in a table containing information for several pathways. We can then sort and filter those pathways to visualize only the top ones. You can select/filter them by either <code>p-value</code> or normalized enrichemnet score (<code>NES</code>).</p>
+<p>Once our list of genes are sorted (from highest to lowest expression in day 7), we can proceed with the enrichment itself. Here, we will be using the <code>fgsea()</code> function. This will result in a table containing information for several pathways. We can then sort and filter those pathways to visualize only the top ones. You can select/filter them by either <code>p-value</code> or normalized enrichment score (<code>NES</code>).</p>
 <div class="chunk-title-parent">
 <div class="chunk-title small">
 R
@@ -509,7 +509,7 @@ <h2><span class="header-section-number">2.2</span> GSEA</h2>
 <ul>
 <li>Which is the most significantly up-regulated pathway at day 7?</li>
 <li>What do the length of the black bars mean?</li>
-<li>Is there any pathway that is significantly down-regulated at 0? Which columns tells you what is Up of downregulated?</li>
+<li>Is there any pathway that is significantly down-regulated at 0?</li>
 <li>Which is the most enriched pathway at day 0?</li>
 <li>What happens if we use <code>-res$log2FoldChange</code> as gene rank ? What changes and why?</li>
 </ul>
@@ -534,12 +534,12 @@ <h2><span class="header-section-number">2.2</span> GSEA</h2>
 <p><i class="fas fa-comments"></i> <strong>Exploratory Questions</strong></p>
 <ul>
 <li>What do the black lines in the X-axis mean?</li>
-<li>By looking at the green line distribution, and the comparison made (day00 - day07), at which time point is this pathways enriched.</li>
+<li>By looking at the green line distribution, and the comparison made (day00 - day07), at which time point is this pathways enriched?</li>
 </ul>
 <p><i class="fas fa-comments"></i> <strong>Exploratory Questions (optional)</strong></p>
 <ul>
 <li>What if instead of the hallmark gene set, you use the GO? Try that.</li>
-<li>How different are the results from EnrichR and GSEA using GO annotation? Remember to use the same comparison (i.e. day07 vs day00).</li>
+<li>How different are the results from EnrichR and GSEA using GO annotation? Remember to use the same comparison (i.e. day00 vs day07).</li>
 </ul>
 </div>
 <div id="online-enrichment-tools" class="section level2" number="2.3">

diff --git a/2403-canvas/lab_functional_files/figure-html/unnamed-chunk-11-1.png b/2403-canvas/lab_functional_files/figure-html/unnamed-chunk-11-1.png
diff --git a/2403-canvas/lab_functional_files/figure-html/unnamed-chunk-12-1.png b/2403-canvas/lab_functional_files/figure-html/unnamed-chunk-12-1.png
diff --git a/2403-canvas/lab_r.html b/2403-canvas/lab_r.html
@@ -405,20 +405,20 @@ <h1><span class="header-section-number">6</span> Functions</h1>
 
 # sort
 sort(x)</code></pre>
-<pre><code>##  [1] 131  37  47  38   9 102 193  34  69  32
+<pre><code>##  [1]  19  76  63  38  73 152 175 134 186 172
 ## [1] 10
-## [1] 692
-## [1] 69.2
-## [1] 42.5
-## [1] 9
-##  [1] 4.875197 3.610918 3.850148 3.637586 2.197225 4.624973 5.262690 3.526361
-##  [9] 4.234107 3.465736
-##  [1] 7.808671e+56 1.171914e+16 2.581313e+20 3.185593e+16 8.103084e+03
-##  [6] 1.986265e+44 6.589235e+83 5.834617e+14 9.253782e+29 7.896296e+13
-##  [1] 11.445523  6.082763  6.855655  6.164414  3.000000 10.099505 13.892444
-##  [8]  5.830952  8.306624  5.656854
-##  [1] 131  37  47  38   9 102 193  34  69  32
-##  [1]   9  32  34  37  38  47  69 102 131 193</code></pre>
+## [1] 1088
+## [1] 108.8
+## [1] 105
+## [1] 19
+##  [1] 2.944439 4.330733 4.143135 3.637586 4.290459 5.023881 5.164786 4.897840
+##  [9] 5.225747 5.147494
+##  [1] 1.784823e+08 1.014800e+33 2.293783e+27 3.185593e+16 5.052394e+31
+##  [6] 1.029820e+66 1.003539e+76 1.568414e+58 6.008605e+80 4.996327e+74
+##  [1]  4.358899  8.717798  7.937254  6.164414  8.544004 12.328828 13.228757
+##  [8] 11.575837 13.638182 13.114877
+##  [1]  19  76  63  38  73 152 175 134 186 172
+##  [1]  19  38  63  73  76 134 152 172 175 186</code></pre>
 <p>Some useful string functions.</p>
 <pre class="r"><code>a &lt;- &quot;sunny&quot;
 b &lt;- &quot;day&quot;

diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-24-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-24-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-25-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-25-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-26-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-26-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-28-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-28-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-29-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-29-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-30-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-30-1.png
diff --git a/2403-canvas/lab_r_files/figure-html/unnamed-chunk-31-1.png b/2403-canvas/lab_r_files/figure-html/unnamed-chunk-31-1.png
diff --git a/2403-canvas/slide_clustering.pdf b/2403-canvas/slide_clustering.pdf
diff --git a/2403-canvas/slide_dge.pdf b/2403-canvas/slide_dge.pdf
diff --git a/2403-canvas/slide_functional.html b/2403-canvas/slide_functional.html
@@ -93,7 +93,9 @@
   - Molecular Function (MF); _Phosphorylation, DNA binding_. 
   - Cellular Component (CC); _Nucleus, Cytoplasm_. 
 - Genes can belong to multiple GO *terms*
-&lt;img src="data/GO_SHOX.png" width="60%" style="display: block; margin: auto;" /&gt;
+
+
+&lt;img src="data/GO_ORA_results.png" width="100%" style="display: block; margin: auto;" /&gt;
 
 ---
 name: pathway1

diff --git a/2403-canvas/slide_functional.pdf b/2403-canvas/slide_functional.pdf
diff --git a/2403-canvas/slide_preprocessing.pdf b/2403-canvas/slide_preprocessing.pdf
diff --git a/2403/Bad_RNASeq_Examples/Bias_GC_Content.jpeg b/2403/Bad_RNASeq_Examples/Bias_GC_Content.jpeg
diff --git a/2403/Bad_RNASeq_Examples/PBAT-base-composition.png b/2403/Bad_RNASeq_Examples/PBAT-base-composition.png
diff --git a/2403/Bad_RNASeq_Examples/Positional sequence bias in random primed libraries.png b/2403/Bad_RNASeq_Examples/Positional sequence bias in random primed libraries.png
diff --git a/2403/Bad_RNASeq_Examples/Technical_Duplication.png b/2403/Bad_RNASeq_Examples/Technical_Duplication.png
diff --git a/2403/Bad_RNASeq_Examples/biased_composition.png b/2403/Bad_RNASeq_Examples/biased_composition.png
diff --git a/2403/Bad_RNASeq_Examples/fastqc_sequence_length_distribution_plot-2-1.png b/2403/Bad_RNASeq_Examples/fastqc_sequence_length_distribution_plot-2-1.png
diff --git a/2403/Bad_RNASeq_Examples/rseqc_inner_distance_plot-1.png b/2403/Bad_RNASeq_Examples/rseqc_inner_distance_plot-1.png
diff --git a/2403/Dockerfile b/2403/Dockerfile
@@ -0,0 +1,42 @@
+# DOCKER FILE FOR WORKSHOP-RNASEQ
+# 2023 Roy Francis
+
+FROM rocker/verse:4.2.3
+LABEL Description="Docker image for NBIS workshop-rnaseq"
+LABEL Maintainer="roy.francis@nbis.se"
+LABEL org.opencontainers.image.source="https://github.com/NBISweden/workshop-rnaseq"
+
+RUN apt-get update -y \
+  && apt-get install --no-install-recommends -y \
+  libxml2-dev \
+  libssl-dev \
+  libcurl4-openssl-dev \
+  libudunits2-dev \
+  libopenblas-base \
+  libgdal-dev \
+  && wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb \
+  && apt-get install -y ./google-chrome-stable_current_amd64.deb \
+  && rm -rf google-chrome-stable_current_amd64.deb \
+  && rm -rf /var/lib/apt/lists/* \
+  && Rscript -e 'install.packages(c("bookdown","knitr","remotes","fontawesome","formattable","kableExtra","leaflet","pagedown","lubridate","markdown","xaringan","yaml"),repos = "https://packagemanager.posit.co/cran/__linux__/jammy/latest");' \
+  && mkdir /rmd
+
+RUN Rscript -e 'install.packages(c("BiocManager","dplyr","enrichR","ggplot2","gridExtra","pheatmap","pvclust","rafalib","stringr","tidyr","locfit"),repos = "https://packagemanager.posit.co/cran/__linux__/jammy/latest");'
+RUN Rscript -e 'BiocManager::install(c("DESeq2","edgeR","fgsea","biomaRt","GEOquery"));'
+WORKDIR /rmd
+CMD Rscript -e "rmarkdown::render_site()"
+
+# build container
+# docker build -t ghcr.io/nbisweden/workshop-rnaseq:1.0.0 .
+# docker tag ghcr.io/nbisweden/workshop-rnaseq:1.0.0 ghcr.io/nbisweden/workshop-rnaseq:latest
+
+# push to ghcr
+# docker login ghcr.io
+# docker push ghcr.io/nbisweden/workshop-rnaseq:1.0.0
+# docker push ghcr.io/nbisweden/workshop-rnaseq:latest
+
+# run container
+# render all files
+# docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-rnaseq:latest
+# render one file
+# docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-rnaseq:latest Rscript -e 'rmarkdown::render("index.Rmd")'
diff --git a/2403/assets/cover.png b/2403/assets/cover.png
diff --git a/2403/assets/end.png b/2403/assets/end.png
diff --git a/2403/assets/favicon.ico b/2403/assets/favicon.ico
diff --git a/2403/assets/favicon.png b/2403/assets/favicon.png
diff --git a/2403/assets/footer-lab.Rmd b/2403/assets/footer-lab.Rmd
@@ -0,0 +1,35 @@
+---
+title: "&nbsp;"
+---
+
+<footer class="footer">
+<div class="container footer-container">
+<div class="row">
+
+<hr>
+
+<div class="col-sm-8" style="text-align:left;vertical-align:middle;">
+<p class="small" style="color:#bdbdbd;">
+[NBIS](https://nbis.se/) • [SciLifeLab](https://www.scilifelab.se/)
+</p>
+</div>
+
+<div class="col-sm-4" style="text-align:right;vertical-align:middle;">
+<p style="color:#bdbdbd;">
+<span>
+<span class="footericon" style="padding-right:4px; padding-left:4px">
+<a href="https://nbis.se/">`r fontawesome::fa("globe-americas",fill="#bdbdbd")`</a>
+</span>
+<span class="footericon" style="padding-right:4px; padding-left:4px">
+<a href="https://twitter.com/NBISwe">`r fontawesome::fa("twitter",fill="#bdbdbd")`</a>
+</span>
+<span class="footericon" style="padding-left:4px">
+<a href="https://www.linkedin.com/company/nbisweden/">`r fontawesome::fa("linkedin",fill="#bdbdbd")`</a>
+</span>
+</span>
+</p>
+</div>
+
+</div>
+</div>
+</footer>
diff --git a/2403/assets/footer-lab.html b/2403/assets/footer-lab.html
@@ -0,0 +1,38 @@
+
+<footer class="footer">
+<div class="container footer-container">
+<div class="row">
+
+<div class="footer-left col-sm-6">
+<p class="small">
+<b>2024</b> • <a href="https://nbis.se/">NBIS</a> • <a href="https://www.scilifelab.se/">SciLifeLab</a>
+</p>
+</div>
+
+<div class="footer-right col-sm-6">
+<p>
+<span>
+  <span class="footericon" style="padding-right:4px; padding-left:4px">
+    <a href="https://nbis.se/">
+      <svg style="height:0.8em;top:.04em;position:relative;fill:#bdbdbd;" viewBox="0 0 496 512"><path d="M248 8C111.03 8 0 119.03 0 256s111.03 248 248 248 248-111.03 248-248S384.97 8 248 8zm82.29 357.6c-3.9 3.88-7.99 7.95-11.31 11.28-2.99 3-5.1 6.7-6.17 10.71-1.51 5.66-2.73 11.38-4.77 16.87l-17.39 46.85c-13.76 3-28 4.69-42.65 4.69v-27.38c1.69-12.62-7.64-36.26-22.63-51.25-6-6-9.37-14.14-9.37-22.63v-32.01c0-11.64-6.27-22.34-16.46-27.97-14.37-7.95-34.81-19.06-48.81-26.11-11.48-5.78-22.1-13.14-31.65-21.75l-.8-.72a114.792 114.792 0 0 1-18.06-20.74c-9.38-13.77-24.66-36.42-34.59-51.14 20.47-45.5 57.36-82.04 103.2-101.89l24.01 12.01C203.48 89.74 216 82.01 216 70.11v-11.3c7.99-1.29 16.12-2.11 24.39-2.42l28.3 28.3c6.25 6.25 6.25 16.38 0 22.63L264 112l-10.34 10.34c-3.12 3.12-3.12 8.19 0 11.31l4.69 4.69c3.12 3.12 3.12 8.19 0 11.31l-8 8a8.008 8.008 0 0 1-5.66 2.34h-8.99c-2.08 0-4.08.81-5.58 2.27l-9.92 9.65a8.008 8.008 0 0 0-1.58 9.31l15.59 31.19c2.66 5.32-1.21 11.58-7.15 11.58h-5.64c-1.93 0-3.79-.7-5.24-1.96l-9.28-8.06a16.017 16.017 0 0 0-15.55-3.1l-31.17 10.39a11.95 11.95 0 0 0-8.17 11.34c0 4.53 2.56 8.66 6.61 10.69l11.08 5.54c9.41 4.71 19.79 7.16 30.31 7.16s22.59 27.29 32 32h66.75c8.49 0 16.62 3.37 22.63 9.37l13.69 13.69a30.503 30.503 0 0 1 8.93 21.57 46.536 46.536 0 0 1-13.72 32.98zM417 274.25c-5.79-1.45-10.84-5-14.15-9.97l-17.98-26.97a23.97 23.97 0 0 1 0-26.62l19.59-29.38c2.32-3.47 5.5-6.29 9.24-8.15l12.98-6.49C440.2 193.59 448 223.87 448 256c0 8.67-.74 17.16-1.82 25.54L417 274.25z"></path>
+      </svg>
+    </a>
+    </span>
+    <span class="footericon" style="padding-right:4px; padding-left:4px">
+      <a href="https://twitter.com/NBISwe"><svg style="height:0.8em;top:.04em;position:relative;fill:#bdbdbd;" viewBox="0 0 512 512"><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path>
+    </svg>
+    </a>
+    </span>
+    <span class="footericon" style="padding-left:4px">
+      <a href="https://www.linkedin.com/company/nbisweden/">
+        <svg style="height:0.8em;top:.04em;position:relative;fill:#bdbdbd;" viewBox="0 0 448 512"><path d="M416 32H31.9C14.3 32 0 46.5 0 64.3v383.4C0 465.5 14.3 480 31.9 480H416c17.6 0 32-14.5 32-32.3V64.3c0-17.8-14.4-32.3-32-32.3zM135.4 416H69V202.2h66.5V416zm-33.2-243c-21.3 0-38.5-17.3-38.5-38.5S80.9 96 102.2 96c21.2 0 38.5 17.3 38.5 38.5 0 21.3-17.2 38.5-38.5 38.5zm282.1 243h-66.4V312c0-24.8-.5-56.7-34.5-56.7-34.6 0-39.9 27-39.9 54.9V416h-66.4V202.2h63.7v29.2h.9c8.9-16.8 30.6-34.5 62.9-34.5 67.2 0 79.7 44.3 79.7 101.9V416z"></path>
+        </svg>
+    </a>
+    </span>
+  </span>
+</p>
+</div>
+
+</div>
+</div>
+</footer>
diff --git a/2403/assets/footer-slide.Rmd b/2403/assets/footer-slide.Rmd
@@ -0,0 +1,6 @@
+.end-text[
+<p class="smaller">
+<span class="small" style="line-height: 1.2;">Graphics from </span><img src="./assets/freepik.jpg" style="max-height:20px; vertical-align:middle;"><br>
+`r paste0("Created: ",format(Sys.time(),format='%d-%b-%Y'))` • <a href="https://www.scilifelab.se/">SciLifeLab</a> • <a href="https://nbis.se/">NBIS</a> 
+</p>
+]
diff --git a/2403/assets/freepik.jpg b/2403/assets/freepik.jpg
diff --git a/2403/assets/header-lab.Rmd b/2403/assets/header-lab.Rmd
@@ -0,0 +1,114 @@
+<!-- rmd lab header -->
+
+```{r,include=FALSE,cache=FALSE}
+# load libraries
+library(knitr) # runs pandoc
+library(bookdown) # for markdown
+library(fontawesome) # icons
+
+# fontawesome dependency
+fa <- rmarkdown::html_dependency_font_awesome()
+fa$attachment <- "fonts/fontawesome-webfont.ttf"
+htmltools::tagList(fa)
+
+# turn off terminal colors
+options(crayon.enabled = FALSE)
+
+# knitr options
+knitr::opts_knit$set(progress=TRUE,verbose=TRUE)
+knitr::opts_chunk$set(dev="png",fig.retina=2,results="hold",fig.show="hold",fig.align="left",
+                      echo=TRUE,warning=FALSE,message=FALSE,accordion=NULL,
+                      chunk.title=NULL)
+color_primary <- "#95b540"
+color_text <- "#424949"
+```
+
+```{r,include=FALSE,cache=FALSE}
+# custom hooks
+## collapsible panel
+knitr::knit_hooks$set(accordion=function(before,options,envir) {
+  if(before) {
+    id <- paste0("acc",format(Sys.time(),"%Y%m%d%H%S"),sample(c(0:9),1),sample(c(0:9),1),sample(c(0:9),1),sample(c(0:9),1))
+    if(is.null(options$btn.type)) {btn.type <- "normal"}else{btn.type <- options$btn.type}
+    paste0('<p>',
+          '<button class="btn btn-sm btn-primary btn-collapse btn-collapse-',btn.type,' collapsed" type="button" data-toggle="collapse" data-target="#',id,'" aria-expanded="false" aria-controls="',id,'">',
+          '</button>',
+          '</p>',
+          '<div class="collapse" id="',id,'">',
+          '<div class="card card-body">')
+  }else{
+    paste0("</div>","</div>")
+  }
+})
+
+## blur panel
+knitr::knit_hooks$set(blur=function(before,options,envir) {
+  if(before) {
+    if(is.null(options$blur.title)) {blur.title <- ""}else{blur.title <- options$blur.title}
+    paste0('<div class="blur-outer">',
+           '<div class="blur-title">',blur.title,'</div>',
+           '<div class="blur-content">')
+  }else{
+    paste0("</div>","</div>")
+  }
+})
+
+## chunk.title for code
+knitr::knit_hooks$set(chunk.title=function(before,options,envir) {
+
+out_class <- NULL
+if(is.null(options$class.output)) {
+if(options$echo) out_class <- options$engine
+if((!options$echo) & (options$results != "hide")) out_class <- "Output"
+}else{
+  out_class <- options$class.output
+}
+
+  if(before) {
+    paste0('<div class="chunk-title-parent"><div class="chunk-title small">',out_class,'</div>')
+  }else{
+    paste0('</div>')
+  }
+})
+
+# knit engine output
+
+eng_output <- function(options) {
+  out <- ''
+  engine_output(options, options$code, out)
+}
+
+knitr::knit_engines$set(output=eng_output)
+
+# custom fontawesome fa function
+fa1 <- function (name=NULL,style="height:0.8em;top:0.04em;position:relative;fill:#424949;",extra_style=NULL)
+{
+    full_name <- NULL
+    if (name %in% fontawesome:::fa_tbl$full_name) {
+        svg <- fontawesome:::fa_tbl[which(fontawesome:::fa_tbl$full_name == name), ][1, 4]
+    }
+    else if (name %in% fontawesome:::fa_tbl$name) {
+        svg <- fontawesome:::fa_tbl[which(fontawesome:::fa_tbl$name == name), ][1, 4]
+    }
+    else {
+        return("")
+    }
+
+    if(!is.null(extra_style)) style <- paste0(style,extra_style)
+    style <- paste0("style=\"", style, "\"")
+
+    if (!grepl(style, pattern = "style=\"\"")) {
+        svg <- gsub(pattern = "^<svg", replacement = paste0("<svg ",
+            style), x = svg)
+    }
+    svg <- htmltools::HTML(svg)
+    class(svg) <- c("fontawesome", class(svg))
+    return(paste0("<span>",svg,"</span>"))
+}
+
+fa2 <- function(name=NULL,style="height:0.8em;top:0.04em;position:relative;fill:white;margin-left:0.45em;margin-bottom: 0.1em;") {
+  return(fa1(name,style))
+}
+```
+
+<br>
diff --git a/2403/assets/header-slide.Rmd b/2403/assets/header-slide.Rmd
@@ -0,0 +1,27 @@
+<link href="https://fonts.googleapis.com/css?family=Roboto|Source+Sans+Pro:300,400,600|Ubuntu+Mono&amp;subset=latin-ext" rel="stylesheet">
+<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous">
+
+```{r,include=FALSE,eval=knitr::opts_knit$get("rmarkdown.pandoc.to")=="html"}
+# Enables Font Awesome in HTML based bookdown outputs.
+fa <- rmarkdown::html_dependency_font_awesome()
+fa$attachment <- "fonts/fontawesome-webfont.ttf"
+htmltools::tagList(fa)
+```
+
+```{r,echo=FALSE,message=FALSE,warning=FALSE,results='hide'}
+# run setup code
+
+# load libraries
+library(knitr) # runs pandoc
+library(bookdown) # for markdown
+
+color_primary <- "#95b540"
+color_text <- "#424949"
+
+# turn off terminal colors
+options(crayon.enabled = FALSE)
+
+# knitr options
+knitr::opts_knit$set(progress=TRUE,verbose=TRUE)
+knitr::opts_chunk$set(dev="png",fig.retina=2,results="hold",fig.show="hold",fig.align="left",echo=TRUE,warning=FALSE,message=FALSE)
+```