GHA: Automated live (rendered) versions of the notebooks

RNA-seq/02-gastric_cancer_tximeta.nb.html

@@ -3298,8 +3298,8 @@ <h2>Summarize to gene</h2>
 <pre class="r"><code># Summarize to the gene level
 gene_summarized &lt;- summarizeToGene(txi_data) </code></pre>
 <!-- rnb-source-end -->
-<!-- rnb-message-begin eyJkYXRhIjoibG9hZGluZyBleGlzdGluZyBFbnNEYiBjcmVhdGVkOiAyMDIyLTA5LTEzIDIxOjM2OjM0XG4ifQ== -->
-<pre><code>loading existing EnsDb created: 2022-09-13 21:36:34</code></pre>
+<!-- rnb-message-begin eyJkYXRhIjoibG9hZGluZyBleGlzdGluZyBFbnNEYiBjcmVhdGVkOiAyMDIyLTEwLTA1IDEyOjU0OjM1XG4ifQ== -->
+<pre><code>loading existing EnsDb created: 2022-10-05 12:54:35</code></pre>
 <!-- rnb-message-end -->
 <!-- rnb-message-begin eyJkYXRhIjoib2J0YWluaW5nIHRyYW5zY3JpcHQtdG8tZ2VuZSBtYXBwaW5nIGZyb20gZGF0YWJhc2VcbiJ9 -->
 <pre><code>obtaining transcript-to-gene mapping from database</code></pre>

intro-to-R-tidyverse/01-intro_to_base_R-live.Rmd

@@ -361,7 +361,7 @@ mean(values_1_to_20)
 
 We have learned functions such as `c`, `length`, `sum`, and etc. 
 Imagine defining a variable called `c`: This will work, but it will lead to a 
-lot of unintended bugs, so its best to avoid this. 
+lot of unintended bugs, so it's best to avoid this. 
 
 ### The `%in%` logical operator 
 

intro-to-R-tidyverse/02-intro_to_ggplot2-live.Rmd

@@ -163,6 +163,8 @@ Remember, the name of this package is `ggplot2`, but the function we use is call
 1. `data`, which is the data frame that contains the data we want to plot.  
 2. `mapping`, which is a special list made with the `aes()` function to describe which values will be used for each **aes**thetic component of the plot, such as the x and y coordinates of each point. 
 (If you find calling things like the x and y coordinates "aesthetics" confusing, don't worry, you are not alone.)  
+Specifically, the `aes()` function is used to specify that a given column (variable) in your data frame be mapped to a given aesthetic component of the plot.
+
 
 ```{r ggplot-base}
 ggplot(
@@ -346,11 +348,17 @@ volcano_plot <- ggplot(
 ```
 
 When we are happy with our plot, we can save the plot using `ggsave`. 
+It's a good idea to also specify `width` and `height` arguments (units in inches)
+to ensure the saved plot is always the same size every time you run this code.
+Here, we'll save a 6"x6" plot.
+
 
 ```{r ggsave}
 ggsave(
   plot = volcano_plot,
-  filename = file.path(plots_dir, "volcano_plot.png")
+  filename = file.path(plots_dir, "volcano_plot.png"),
+  width = 6, 
+  height = 6 
 )
 ```