diff --git a/40-visualization.Rmd b/40-visualization.Rmd
index 56cc634..ec1159c 100644
--- a/40-visualization.Rmd
+++ b/40-visualization.Rmd
@@ -29,7 +29,7 @@ rna <- read.csv("data/rnaseq.csv")
 ```
 
 The [Data Visualization Cheat
-Sheet](https://github.com/rstudio/cheatsheets/raw/main/data-visualization-2.1.pdf)
+Sheet](https://raw.githubusercontent.com/rstudio/cheatsheets/main/data-visualization.pdf)
 will cover the basics and more advanced features of `ggplot2` and will
 help, in addition to serve as a reminder, getting an overview of the
 many data representations available in the package. The following
@@ -70,7 +70,7 @@ graph from the same 3 components: (1) a data set, (2) a coordinate system,
 and (3) geoms — i.e. visual marks that represent data points [^three_comp_ggplot2].
 
 [^three_comp_ggplot2]: Source: [Data Visualization Cheat
-Sheet](https://github.com/rstudio/cheatsheets/raw/main/data-visualization-2.1.pdf).
+Sheet](https://raw.githubusercontent.com/rstudio/cheatsheets/main/data-visualization.pdf).
 
 
 To build a ggplot, we will use the following basic template that can
@@ -718,7 +718,7 @@ themes.
 Let's come back to the faceted plot of mean expression by time and gene, colored by sex.
 
 Take a look at the [**`ggplot2`** cheat
-sheet](https://github.com/rstudio/cheatsheets/blob/master/data-visualization-2.1.pdf)
+sheet](https://raw.githubusercontent.com/rstudio/cheatsheets/main/data-visualization.pdf)
 and think of ways you could improve the plot.
 
 Now, we can change names of axes to something more informative than 'time'
@@ -808,7 +808,7 @@ ggplot(rna, aes(x = expression_log)) +
 With all of this information in hand, please take another five minutes
 to either improve one of the plots generated in this exercise or
 create a beautiful graph of your own. Use the RStudio [`ggplot2` cheat
-sheet](https://github.com/rstudio/cheatsheets/raw/main/data-visualization-2.1.pdf)
+sheet](https://raw.githubusercontent.com/rstudio/cheatsheets/main/data-visualization.pdf)
 for inspiration. Here are some ideas:
 
 - See if you can change the thickness of the lines.
@@ -1026,16 +1026,6 @@ ggsave("fig_output/combo_plot_chromosome_sex.png", combo_plot,
 Note: The parameters `width` and `height` also determine the font size
 in the saved plot.
 
-
-```{r final-challenge, eval=FALSE, purl=TRUE, echo=FALSE}
-### Final plotting challenge:
-##  With all of this information in hand, please take another five
-##  minutes to either improve one of the plots generated in this
-##  exercise or create a beautiful graph of your own. Use the RStudio
-##  ggplot2 cheat sheet for inspiration:
-##  https://www.rstudio.com/wp-content/uploads/2015/08/ggplot2-cheatsheet.pdf
-```
-
 ## Other packages for visualisation
 
 `ggplot2` is a very powerful package that fits very nicely in our
diff --git a/60-rr.Rmd b/60-rr.Rmd
index bda8415..e779be8 100644
--- a/60-rr.Rmd
+++ b/60-rr.Rmd
@@ -207,9 +207,9 @@ rendered. Finish your report with a *Session information* section.
 `r msmbstyle::question_end()`
 
 The [R Markdown Cheat
-Sheet](https://github.com/rstudio/cheatsheets/raw/main/rmarkdown-2.0.pdf)
+Sheet](https://raw.githubusercontent.com/rstudio/cheatsheets/main/rmarkdown.pdf)
 and [Reference
-Guide](https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf)
+Guide](https://www.dataquest.io/blog/r-markdown-guide-cheatsheet/)
 will help you with the markdown synatax, R code chunk options, and
 RStudio utlisation.
 
diff --git a/docs/404.html b/docs/404.html
index d65ae29..111b2c0 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -217,7 +217,7 @@ <h1>Page not found</h1>
 <p style="text-align: center;">
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/index.html b/docs/index.html
index 595c583..74cc669 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -459,7 +459,7 @@ <h2>Setup<div class="tooltip"><button class="internal-link-btn" onclick="copy_li
 <a href="sec-dataorg.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-anx.html b/docs/sec-anx.html
index 62a6c08..4d4b757 100644
--- a/docs/sec-anx.html
+++ b/docs/sec-anx.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -491,7 +491,7 @@ <h2>
 <a href="session-information.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-bioinfo.html b/docs/sec-bioinfo.html
index c62d9b3..811c84a 100644
--- a/docs/sec-bioinfo.html
+++ b/docs/sec-bioinfo.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -1149,7 +1149,7 @@ <h2>
 <a href="sec-prog.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-ccl.html b/docs/sec-ccl.html
index 8687901..8902cbd 100644
--- a/docs/sec-ccl.html
+++ b/docs/sec-ccl.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -333,7 +333,7 @@ <h2>
 <a href="sec-anx.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-dataorg.html b/docs/sec-dataorg.html
index 29b76bb..ccebfcc 100644
--- a/docs/sec-dataorg.html
+++ b/docs/sec-dataorg.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -1133,7 +1133,7 @@ <h2>
 <a href="sec-rrstudio.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-dplyr.html b/docs/sec-dplyr.html
index 56a430e..3ec587d 100644
--- a/docs/sec-dplyr.html
+++ b/docs/sec-dplyr.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -318,7 +318,7 @@ <h2>
 tidyverse package <strong><code>readr</code></strong>, instead of <code>read.csv()</code>.</p>
 <div class="sourceCode" id="cb300"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb300-1"><a href="sec-dplyr.html#cb300-1" tabindex="-1"></a>rna <span class="ot">&lt;-</span> <span class="fu">read_csv</span>(<span class="st">"data/rnaseq.csv"</span>)</span></code></pre></div>
 <pre><code>## Rows: 32428 Columns: 19
-## ── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (14): gene, sample, organism, sex, infection, strain, tissue, product, e...
 ## dbl  (5): expression, age, time, mouse, ENTREZID
@@ -914,8 +914,8 @@ <h3>
 <div class="sourceCode" id="cb349"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb349-1"><a href="sec-dplyr.html#cb349-1" tabindex="-1"></a>rna <span class="sc">%&gt;%</span></span>
 <span id="cb349-2"><a href="sec-dplyr.html#cb349-2" tabindex="-1"></a>  <span class="fu">group_by</span>(gene, infection, time) <span class="sc">%&gt;%</span></span>
 <span id="cb349-3"><a href="sec-dplyr.html#cb349-3" tabindex="-1"></a>  <span class="fu">summarize</span>(<span class="at">mean_expression =</span> <span class="fu">mean</span>(expression))</span></code></pre></div>
-<pre><code>## `summarise()` has grouped output by 'gene', 'infection'. You can override using
-## the `.groups` argument.</code></pre>
+<pre><code>## `summarise()` has grouped output by 'gene', 'infection'. You can override using the `.groups`
+## argument.</code></pre>
 <pre><code>## # A tibble: 4,422 × 4
 ## # Groups:   gene, infection [2,948]
 ##    gene     infection    time mean_expression
@@ -939,8 +939,8 @@ <h3>
 <span id="cb352-2"><a href="sec-dplyr.html#cb352-2" tabindex="-1"></a>  <span class="fu">group_by</span>(gene, infection, time) <span class="sc">%&gt;%</span></span>
 <span id="cb352-3"><a href="sec-dplyr.html#cb352-3" tabindex="-1"></a>  <span class="fu">summarize</span>(<span class="at">mean_expression =</span> <span class="fu">mean</span>(expression)) <span class="sc">%&gt;%</span></span>
 <span id="cb352-4"><a href="sec-dplyr.html#cb352-4" tabindex="-1"></a>  <span class="fu">print</span>(<span class="at">n =</span> <span class="dv">15</span>)</span></code></pre></div>
-<pre><code>## `summarise()` has grouped output by 'gene', 'infection'. You can override using
-## the `.groups` argument.</code></pre>
+<pre><code>## `summarise()` has grouped output by 'gene', 'infection'. You can override using the `.groups`
+## argument.</code></pre>
 <pre><code>## # A tibble: 4,422 × 4
 ## # Groups:   gene, infection [2,948]
 ##    gene     infection    time mean_expression
@@ -968,8 +968,8 @@ <h3>
 <span id="cb355-2"><a href="sec-dplyr.html#cb355-2" tabindex="-1"></a>  <span class="fu">group_by</span>(gene, infection, time) <span class="sc">%&gt;%</span></span>
 <span id="cb355-3"><a href="sec-dplyr.html#cb355-3" tabindex="-1"></a>  <span class="fu">summarize</span>(<span class="at">mean_expression =</span> <span class="fu">mean</span>(expression),</span>
 <span id="cb355-4"><a href="sec-dplyr.html#cb355-4" tabindex="-1"></a>            <span class="at">median_expression =</span> <span class="fu">median</span>(expression))</span></code></pre></div>
-<pre><code>## `summarise()` has grouped output by 'gene', 'infection'. You can override using
-## the `.groups` argument.</code></pre>
+<pre><code>## `summarise()` has grouped output by 'gene', 'infection'. You can override using the `.groups`
+## argument.</code></pre>
 <pre><code>## # A tibble: 4,422 × 5
 ## # Groups:   gene, infection [2,948]
 ##    gene     infection    time mean_expression median_expression
@@ -992,8 +992,8 @@ <h3>
 <span id="cb358-3"><a href="sec-dplyr.html#cb358-3" tabindex="-1"></a>  <span class="fu">summarize</span>(<span class="at">mean_expression =</span> <span class="fu">mean</span>(expression),</span>
 <span id="cb358-4"><a href="sec-dplyr.html#cb358-4" tabindex="-1"></a>            <span class="at">median_expression =</span> <span class="fu">median</span>(expression)) <span class="sc">%&gt;%</span></span>
 <span id="cb358-5"><a href="sec-dplyr.html#cb358-5" tabindex="-1"></a>  <span class="fu">arrange</span>(mean_expression)</span></code></pre></div>
-<pre><code>## `summarise()` has grouped output by 'gene', 'infection'. You can override using
-## the `.groups` argument.</code></pre>
+<pre><code>## `summarise()` has grouped output by 'gene', 'infection'. You can override using the `.groups`
+## argument.</code></pre>
 <pre><code>## # A tibble: 4,422 × 5
 ## # Groups:   gene, infection [2,948]
 ##    gene    infection    time mean_expression median_expression
@@ -1015,8 +1015,8 @@ <h3>
 <span id="cb361-3"><a href="sec-dplyr.html#cb361-3" tabindex="-1"></a>  <span class="fu">summarize</span>(<span class="at">mean_expression =</span> <span class="fu">mean</span>(expression),</span>
 <span id="cb361-4"><a href="sec-dplyr.html#cb361-4" tabindex="-1"></a>            <span class="at">median_expression =</span> <span class="fu">median</span>(expression)) <span class="sc">%&gt;%</span></span>
 <span id="cb361-5"><a href="sec-dplyr.html#cb361-5" tabindex="-1"></a>  <span class="fu">arrange</span>(<span class="fu">desc</span>(mean_expression))</span></code></pre></div>
-<pre><code>## `summarise()` has grouped output by 'gene', 'infection'. You can override using
-## the `.groups` argument.</code></pre>
+<pre><code>## `summarise()` has grouped output by 'gene', 'infection'. You can override using the `.groups`
+## argument.</code></pre>
 <pre><code>## # A tibble: 4,422 × 5
 ## # Groups:   gene, infection [2,948]
 ##    gene   infection    time mean_expression median_expression
@@ -2013,7 +2013,7 @@ <h2>
 <a href="sec-vis.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-join.html b/docs/sec-join.html
index c945b2d..672581c 100644
--- a/docs/sec-join.html
+++ b/docs/sec-join.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -559,7 +559,8 @@ <h2>
 <pre><code>## Warning in inner_join(jdf6, jdf7): Detected an unexpected many-to-many relationship between `x` and `y`.
 ## ℹ Row 2 of `x` matches multiple rows in `y`.
 ## ℹ Row 1 of `y` matches multiple rows in `x`.
-## ℹ If a many-to-many relationship is expected, set `relationship = "many-to-many"` to silence this warning.</code></pre>
+## ℹ If a many-to-many relationship is expected, set `relationship = "many-to-many"` to silence
+##   this warning.</code></pre>
 <pre><code>## # A tibble: 4 × 9
 ##   uniprot organelle     entry isoform gene_name description organism isoform_num
 ##   &lt;chr&gt;   &lt;chr&gt;         &lt;chr&gt;   &lt;dbl&gt; &lt;chr&gt;     &lt;chr&gt;       &lt;chr&gt;          &lt;dbl&gt;
@@ -835,7 +836,7 @@ <h2>
 <a href="sec-rr.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-prog.html b/docs/sec-prog.html
index 56340ab..3749e90 100644
--- a/docs/sec-prog.html
+++ b/docs/sec-prog.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -471,7 +471,7 @@ <h3>Which iteration to use?<div class="tooltip"><button class="internal-link-btn
 <span id="cb659-3"><a href="sec-prog.html#cb659-3" tabindex="-1"></a>fls <span class="ot">&lt;-</span> <span class="fu">expressions.csv</span>()</span>
 <span id="cb659-4"><a href="sec-prog.html#cb659-4" tabindex="-1"></a><span class="fu">read_csv</span>(fls[<span class="dv">1</span>])</span></code></pre></div>
 <pre><code>## Rows: 570 Columns: 4
-## ── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (3): sampleID, patient, type
 ## dbl (1): A1BG
@@ -494,7 +494,7 @@ <h3>Which iteration to use?<div class="tooltip"><button class="internal-link-btn
 ## # ℹ 560 more rows</code></pre>
 <div class="sourceCode" id="cb662"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb662-1"><a href="sec-prog.html#cb662-1" tabindex="-1"></a><span class="fu">read_csv</span>(fls[<span class="dv">2</span>])</span></code></pre></div>
 <pre><code>## Rows: 570 Columns: 4
-## ── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (3): sampleID, patient, type
 ## dbl (1): A1CF
@@ -691,7 +691,7 @@ <h2>
 ##     }
 ##     return(sum(res))
 ## }
-## &lt;bytecode: 0x5631e5674c70&gt;</code></pre>
+## &lt;bytecode: 0x556a6b250430&gt;</code></pre>
 <div class="sourceCode" id="cb694"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb694-1"><a href="sec-prog.html#cb694-1" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">1</span><span class="dt">L</span>)</span>
 <span id="cb694-2"><a href="sec-prog.html#cb694-2" tabindex="-1"></a><span class="fu">fun</span>(<span class="dv">5</span>, <span class="dv">15</span>)</span></code></pre></div>
 <pre><code>## [1] 4825.278</code></pre>
@@ -827,7 +827,7 @@ <h2>
 <span id="cb721-2"><a href="sec-prog.html#cb721-2" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="fu">seq_along</span>(fls))</span>
 <span id="cb721-3"><a href="sec-prog.html#cb721-3" tabindex="-1"></a>    l[[i]] <span class="ot">&lt;-</span> <span class="fu">read_csv</span>(fls[i])</span></code></pre></div>
 <pre><code>## Rows: 100 Columns: 8
-## ── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (2): id, gender
 ## dbl (6): height, X, interro1, interro2, interro3, interro4
@@ -835,7 +835,7 @@ <h2>
 ## ℹ Use `spec()` to retrieve the full column specification for this data.
 ## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
 ## Rows: 105 Columns: 8
-## ── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (2): id, gender
 ## dbl (6): height, X, interro1, interro2, interro3, interro4
@@ -863,7 +863,7 @@ <h2>
 <p>or</p>
 <div class="sourceCode" id="cb727"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb727-1"><a href="sec-prog.html#cb727-1" tabindex="-1"></a>l <span class="ot">&lt;-</span> <span class="fu">lapply</span>(fls, read_csv)</span></code></pre></div>
 <pre><code>## Rows: 100 Columns: 8
-## ── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (2): id, gender
 ## dbl (6): height, X, interro1, interro2, interro3, interro4
@@ -871,7 +871,7 @@ <h2>
 ## ℹ Use `spec()` to retrieve the full column specification for this data.
 ## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
 ## Rows: 105 Columns: 8
-## ── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (2): id, gender
 ## dbl (6): height, X, interro1, interro2, interro3, interro4
@@ -1111,7 +1111,7 @@ <h2>
 <a href="sec-ccl.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-rr.html b/docs/sec-rr.html
index e525ff9..2294800 100644
--- a/docs/sec-rr.html
+++ b/docs/sec-rr.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -412,9 +412,9 @@ <h2>
 </p>
 </div>
 </div>
-<p>The <a href="https://github.com/rstudio/cheatsheets/raw/main/rmarkdown-2.0.pdf">R Markdown Cheat
+<p>The <a href="https://raw.githubusercontent.com/rstudio/cheatsheets/main/rmarkdown.pdf">R Markdown Cheat
 Sheet</a>
-and <a href="https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf">Reference
+and <a href="https://www.dataquest.io/blog/r-markdown-guide-cheatsheet/">Reference
 Guide</a>
 will help you with the markdown synatax, R code chunk options, and
 RStudio utlisation.</p>
@@ -549,7 +549,7 @@ <h2>
 <a href="sec-bioinfo.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-rrstudio.html b/docs/sec-rrstudio.html
index f7e2d7d..84ef4da 100644
--- a/docs/sec-rrstudio.html
+++ b/docs/sec-rrstudio.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -910,7 +910,7 @@ <h3>
 <a href="sec-startr.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-startdata.html b/docs/sec-startdata.html
index 2712d07..1801084 100644
--- a/docs/sec-startdata.html
+++ b/docs/sec-startdata.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
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@@ -1730,7 +1730,7 @@ <h2>
 <a href="sec-dplyr.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-startr.html b/docs/sec-startr.html
index 3cd22c4..b86ce98 100644
--- a/docs/sec-startr.html
+++ b/docs/sec-startr.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -1341,7 +1341,7 @@ <h2>
 <a href="sec-startdata.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/sec-vis.html b/docs/sec-vis.html
index 9c4aa5b..d3da90c 100644
--- a/docs/sec-vis.html
+++ b/docs/sec-vis.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -237,7 +237,7 @@ <h1>
 <div class="sourceCode" id="cb439"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb439-1"><a href="sec-vis.html#cb439-1" tabindex="-1"></a><span class="fu">library</span>(<span class="st">"tidyverse"</span>)</span></code></pre></div>
 <p>If not still in the workspace, load the data we saved in the previous lesson.</p>
 <div class="sourceCode" id="cb440"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb440-1"><a href="sec-vis.html#cb440-1" tabindex="-1"></a>rna <span class="ot">&lt;-</span> <span class="fu">read.csv</span>(<span class="st">"data/rnaseq.csv"</span>)</span></code></pre></div>
-<p>The <a href="https://github.com/rstudio/cheatsheets/raw/main/data-visualization-2.1.pdf">Data Visualization Cheat
+<p>The <a href="https://raw.githubusercontent.com/rstudio/cheatsheets/main/data-visualization.pdf">Data Visualization Cheat
 Sheet</a>
 will cover the basics and more advanced features of <code>ggplot2</code> and will
 help, in addition to serve as a reminder, getting an overview of the
@@ -441,8 +441,8 @@ <h2>
 <span id="cb459-5"><a href="sec-vis.html#cb459-5" tabindex="-1"></a>  <span class="fu">pivot_wider</span>(<span class="at">names_from =</span> time,</span>
 <span id="cb459-6"><a href="sec-vis.html#cb459-6" tabindex="-1"></a>              <span class="at">values_from =</span> mean_exp) <span class="sc">%&gt;%</span></span>
 <span id="cb459-7"><a href="sec-vis.html#cb459-7" tabindex="-1"></a>  <span class="fu">mutate</span>(<span class="at">time_8_vs_0 =</span> <span class="st">`</span><span class="at">8</span><span class="st">`</span> <span class="sc">-</span> <span class="st">`</span><span class="at">0</span><span class="st">`</span>, <span class="at">time_4_vs_0 =</span> <span class="st">`</span><span class="at">4</span><span class="st">`</span> <span class="sc">-</span> <span class="st">`</span><span class="at">0</span><span class="st">`</span>)</span></code></pre></div>
-<pre><code>## `summarise()` has grouped output by 'gene', 'time'. You can override using the
-## `.groups` argument.</code></pre>
+<pre><code>## `summarise()` has grouped output by 'gene', 'time'. You can override using the `.groups`
+## argument.</code></pre>
 <p>We can then build a ggplot with the newly created dataset
 <code>rna_fc</code>. Building plots with <code>ggplot2</code> is typically an iterative
 process. We start by defining the dataset we’ll use, lay out the axes,
@@ -825,8 +825,8 @@ <h2>
 <div class="sourceCode" id="cb498"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb498-1"><a href="sec-vis.html#cb498-1" tabindex="-1"></a>mean_exp_by_time_sex <span class="ot">&lt;-</span> sub_rna <span class="sc">%&gt;%</span></span>
 <span id="cb498-2"><a href="sec-vis.html#cb498-2" tabindex="-1"></a>  <span class="fu">group_by</span>(gene, time, sex) <span class="sc">%&gt;%</span></span>
 <span id="cb498-3"><a href="sec-vis.html#cb498-3" tabindex="-1"></a>  <span class="fu">summarize</span>(<span class="at">mean_exp =</span> <span class="fu">mean</span>(expression_log))</span></code></pre></div>
-<pre><code>## `summarise()` has grouped output by 'gene', 'time'. You can override using the
-## `.groups` argument.</code></pre>
+<pre><code>## `summarise()` has grouped output by 'gene', 'time'. You can override using the `.groups`
+## argument.</code></pre>
 <p>We can now make the faceted plot by splitting further by sex using
 <code>color</code> (within a single plot):</p>
 <div class="sourceCode" id="cb500"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb500-1"><a href="sec-vis.html#cb500-1" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="at">data =</span> mean_exp_by_time_sex,</span>
@@ -871,8 +871,8 @@ <h2>
 <div class="sourceCode" id="cb504"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb504-1"><a href="sec-vis.html#cb504-1" tabindex="-1"></a>mean_exp_by_chromosome <span class="ot">&lt;-</span> rna <span class="sc">%&gt;%</span></span>
 <span id="cb504-2"><a href="sec-vis.html#cb504-2" tabindex="-1"></a>  <span class="fu">group_by</span>(chromosome_name, time) <span class="sc">%&gt;%</span></span>
 <span id="cb504-3"><a href="sec-vis.html#cb504-3" tabindex="-1"></a>  <span class="fu">summarize</span>(<span class="at">mean_exp =</span> <span class="fu">mean</span>(expression_log))</span></code></pre></div>
-<pre><code>## `summarise()` has grouped output by 'chromosome_name'. You can override using
-## the `.groups` argument.</code></pre>
+<pre><code>## `summarise()` has grouped output by 'chromosome_name'. You can override using the `.groups`
+## argument.</code></pre>
 <div class="sourceCode" id="cb506"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb506-1"><a href="sec-vis.html#cb506-1" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="at">data =</span> mean_exp_by_chromosome,</span>
 <span id="cb506-2"><a href="sec-vis.html#cb506-2" tabindex="-1"></a>       <span class="at">mapping =</span> <span class="fu">aes</span>(<span class="at">x =</span> time,</span>
 <span id="cb506-3"><a href="sec-vis.html#cb506-3" tabindex="-1"></a>                     <span class="at">y =</span> mean_exp)) <span class="sc">+</span></span>
@@ -933,7 +933,7 @@ <h2>
 <span class="header-section-number">6.7</span> Customisation<div class="tooltip"><button class="internal-link-btn" onclick="copy_link('customisation')" onmouseout="reset_tooltip('customisation-tooltip')"><span class="tooltiptext" id="customisation-tooltip">Copy link</span><i class="fa fa-link"></i></button></div>
 </h2>
 <p>Let’s come back to the faceted plot of mean expression by time and gene, colored by sex.</p>
-<p>Take a look at the <a href="https://github.com/rstudio/cheatsheets/blob/master/data-visualization-2.1.pdf"><strong><code>ggplot2</code></strong> cheat
+<p>Take a look at the <a href="https://raw.githubusercontent.com/rstudio/cheatsheets/main/data-visualization.pdf"><strong><code>ggplot2</code></strong> cheat
 sheet</a>
 and think of ways you could improve the plot.</p>
 <p>Now, we can change names of axes to something more informative than ‘time’
@@ -1014,7 +1014,7 @@ <h2>
 <div class="question-body">
 <p>With all of this information in hand, please take another five minutes
 to either improve one of the plots generated in this exercise or
-create a beautiful graph of your own. Use the RStudio <a href="https://github.com/rstudio/cheatsheets/raw/main/data-visualization-2.1.pdf"><code>ggplot2</code> cheat
+create a beautiful graph of your own. Use the RStudio <a href="https://raw.githubusercontent.com/rstudio/cheatsheets/main/data-visualization.pdf"><code>ggplot2</code> cheat
 sheet</a>
 for inspiration. Here are some ideas:</p>
 <ul>
@@ -1415,7 +1415,7 @@ <h2>
 <div class="footnotes">
 <hr>
 <ol start="10">
-<li id="fn10"><p>Source: <a href="https://github.com/rstudio/cheatsheets/raw/main/data-visualization-2.1.pdf">Data Visualization Cheat
+<li id="fn10"><p>Source: <a href="https://raw.githubusercontent.com/rstudio/cheatsheets/main/data-visualization.pdf">Data Visualization Cheat
 Sheet</a>.<a href="sec-vis.html#fnref10" class="footnote-back">↩︎</a></p></li>
 </ol>
 </div>
@@ -1426,7 +1426,7 @@ <h2>
 <a href="sec-join.html"><button class="btn btn-default">Next</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>
diff --git a/docs/session-information.html b/docs/session-information.html
index 1f5ab8f..0185ccc 100644
--- a/docs/session-information.html
+++ b/docs/session-information.html
@@ -13,7 +13,7 @@
 
 <meta name="author" content="Laurent Gatto" />
 
-<meta name="date" content="2024-03-13" />
+<meta name="date" content="2024-03-15" />
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -300,7 +300,7 @@ <h2>
 <a href="sec-anx.html"><button class="btn btn-default">Previous</button></a>
 </p>
 <p class="build-date">Page built: 
-2024-03-13
+2024-03-15
  using 
 R version 4.3.2 Patched (2023-12-27 r85757)
 </p>