Update to R 4.4. and bioc 3.19

.github/workflows/quarto.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: ✅ Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: 🆀 Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2

_freeze/course-info/final-projects/execute-results/html.json

@@ -1,7 +1,8 @@
 {
-  "hash": "43fe8b6d7bb6a8f25c6b170f5a0dfae2",
+  "hash": "2a3e207e8951f963c66aaea78321e3cb",
   "result": {
-    "markdown": "---\ntitle: \"MOLB 7950 -- Final Projects\"\neditor: \n  markdown: \n    wrap: 72\n---\n\n\n## Short proposal\n\nPlease submit a short proposal for your final projects with the\nfollowing information.\n\n-   the names of people you are working with\n\n-   a description of the data set you will be working worth. This can\n    refer to a publication and/or contain a link to public data\n    available at NCBI GEO.\n\n-   a hypothesis (tentative) you will be testing\n\n-   a few bullets on your planned analysis approach.\n\nPlease include this information in a quarto document in a new Posit\ncloud project.\n\n## Overview\n\n-   Final projects can involve groups of 1-3 people.\n\n-   Projects are choose your own adventure:\n\n    1.  The [resource documents](resources/block-dna-resources.qmd)\n        contain data sets in from human S. cerevisiae. For example,\n        sub-nucleosomal fragments provide a DNA-based signal to\n        understand chromatin transactions that lead to transcription.\n\n    2.  You could find a data set on [NCBI\n        GEO](https://www.ncbi.nlm.nih.gov/geo/) of interest (e.g.,\n        relevant to your thesis work), and work it up with salmon,\n        DEseq, and exploratory analysis. We are happy to help you work\n        through the pseudo-alignment steps.\n\n    3.  You can start with your own sequencing data (bulk/single-cell\n        RNA seq, DNA sequencing).\n\n## Deliverables\n\n-   A Quarto document with code, plots, interpretations, and next steps.\n\n-   If you work in a group, list the members of the group at the top of\n    the document, and make it clear which parts are your work by adding\n    your initials to code chunks.\n\n-   Short presentations (5-8 minutes) by the groups the week of Nov 1.\n    Presentations should include 1-2 slides of background, a hypothesis\n    for the approach, code output (table or graph) that addresses the\n    hypothesis, and one or more tests of the statistical significance of\n    the observation.\n\n## Grading and rubric\n\nThe final project will be worth 20% of your grade and we will use the\ngrading scheme outlined in the [grading\nrubric](syllabus.qmd#problem-set-rubric).\n\nEach individual in a group will be evaluated separately, so\ncontributions must be clearly marked in the document, using e.g. using\nchunk labels:\n\n\n::: {.cell}\n\n````{.cell-code}\n```{{r}}\n#| label: plotting-code-by-jay-h\n#| eval: false\nggplot(mtcars, aes(hp, mpg)) + geom_point()\n```\n````\n:::\n",
+    "engine": "knitr",
+    "markdown": "---\ntitle: \"MOLB 7950 -- Final Projects\"\neditor: \n  markdown: \n    wrap: 72\n---\n\n\n## Short proposal\n\nPlease submit a short proposal for your final projects with the\nfollowing information.\n\n-   the names of people you are working with\n\n-   a description of the data set you will be working worth. This can\n    refer to a publication and/or contain a link to public data\n    available at NCBI GEO.\n\n-   a hypothesis (tentative) you will be testing\n\n-   a few bullets on your planned analysis approach.\n\nPlease include this information in a quarto document in a new Posit\ncloud project.\n\n## Overview\n\n-   Final projects can involve groups of 1-3 people.\n\n-   Projects are choose your own adventure:\n\n    1.  The [resource documents](/resources/block-dna-resources.qmd)\n        contain data sets in from human S. cerevisiae. For example,\n        sub-nucleosomal fragments provide a DNA-based signal to\n        understand chromatin transactions that lead to transcription.\n\n    2.  You could find a data set on [NCBI\n        GEO](https://www.ncbi.nlm.nih.gov/geo/) of interest (e.g.,\n        relevant to your thesis work), and work it up with salmon,\n        DEseq, and exploratory analysis. We are happy to help you work\n        through the pseudo-alignment steps.\n\n    3.  You can start with your own sequencing data (bulk/single-cell\n        RNA seq, DNA sequencing).\n\n## Deliverables\n\n-   A Quarto document with code, plots, interpretations, and next steps.\n\n-   If you work in a group, list the members of the group at the top of\n    the document, and make it clear which parts are your work by adding\n    your initials to code chunks.\n\n-   Short presentations (5-8 minutes) by the groups the week of Nov 1.\n    Presentations should include 1-2 slides of background, a hypothesis\n    for the approach, code output (table or graph) that addresses the\n    hypothesis, and one or more tests of the statistical significance of\n    the observation.\n\n## Grading and rubric\n\nThe final project will be worth 20% of your grade and we will use the\ngrading scheme outlined in the [grading\nrubric](syllabus.qmd#problem-set-rubric).\n\nEach individual in a group will be evaluated separately, so\ncontributions must be clearly marked in the document, using e.g. using\nchunk labels:\n\n\n::: {.cell}\n\n````{.cell-code}\n```{{r}}\n#| label: plotting-code-by-jay-h\n#| eval: false\nggplot(mtcars, aes(hp, mpg)) + geom_point()\n```\n````\n:::\n",
     "supporting": [
       "final-projects_files"
     ],

_freeze/site_libs/revealjs/plugin/quarto-line-highlight/line-highlight.js

@@ -38,7 +38,7 @@ window.QuartoLineHighlight = function () {
     divSourceCode.forEach((el) => {
       if (el.hasAttribute(kCodeLineNumbersAttr)) {
         const codeLineAttr = el.getAttribute(kCodeLineNumbersAttr);
-        el.removeAttribute("data-code-line-numbers");
+        el.removeAttribute(kCodeLineNumbersAttr);
         if (handleLinesSelector(deck, codeLineAttr)) {
           // Only process if attr is a string to select lines to highlights
           // e.g "1|3,6|8-11"
@@ -165,17 +165,17 @@ window.QuartoLineHighlight = function () {
         if (typeof highlight.last === "number") {
           spanToHighlight = [].slice.call(
             codeBlock.querySelectorAll(
-              ":scope > span:nth-child(n+" +
+              ":scope > span:nth-of-type(n+" +
                 highlight.first +
-                "):nth-child(-n+" +
+                "):nth-of-type(-n+" +
                 highlight.last +
                 ")"
             )
           );
         } else if (typeof highlight.first === "number") {
           spanToHighlight = [].slice.call(
             codeBlock.querySelectorAll(
-              ":scope > span:nth-child(" + highlight.first + ")"
+              ":scope > span:nth-of-type(" + highlight.first + ")"
             )
           );
         }

_freeze/site_libs/revealjs/plugin/quarto-support/support.js

@@ -4,6 +4,20 @@ window.QuartoSupport = function () {
     return /print-pdf/gi.test(window.location.search);
   }
 
+  // helper for theme toggling
+  function toggleBackgroundTheme(el, onDarkBackground, onLightBackground) {
+    if (onDarkBackground) {
+      el.classList.add('has-dark-background')
+    } else {
+      el.classList.remove('has-dark-background')
+    }
+    if (onLightBackground) {
+      el.classList.add('has-light-background')
+    } else {
+      el.classList.remove('has-light-background')
+    }
+  }
+
   // implement controlsAudo
   function controlsAuto(deck) {
     const config = deck.getConfig();
@@ -111,8 +125,19 @@ window.QuartoSupport = function () {
     }
   }
 
-  // add footer text
-  function addFooter(deck) {
+  // tweak slide-number element
+  function tweakSlideNumber(deck) {
+    deck.on("slidechanged", function (ev) {
+      const revealParent = deck.getRevealElement();
+      const slideNumberEl = revealParent.querySelector(".slide-number");
+      const onDarkBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-dark-background');
+      const onLightBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-light-background');
+      toggleBackgroundTheme(slideNumberEl, onDarkBackground, onLightBackground);
+    })
+  }
+
+   // add footer text
+   function addFooter(deck) {
     const revealParent = deck.getRevealElement();
     const defaultFooterDiv = document.querySelector(".footer-default");
     if (defaultFooterDiv) {
@@ -127,13 +152,17 @@ window.QuartoSupport = function () {
             prevSlideFooter.remove();
           }
           const currentSlideFooter = ev.currentSlide.querySelector(".footer");
+          const onDarkBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-dark-background')
+          const onLightBackground = Reveal.getSlideBackground(ev.indexh, ev.indexv).classList.contains('has-light-background')
           if (currentSlideFooter) {
             defaultFooterDiv.style.display = "none";
             const slideFooter = currentSlideFooter.cloneNode(true);
             handleLinkClickEvents(deck, slideFooter);
             deck.getRevealElement().appendChild(slideFooter);
+            toggleBackgroundTheme(slideFooter, onDarkBackground, onLightBackground)
           } else {
             defaultFooterDiv.style.display = "block";
+            toggleBackgroundTheme(defaultFooterDiv, onDarkBackground, onLightBackground)
           }
         });
       }
@@ -280,6 +309,7 @@ window.QuartoSupport = function () {
       fixupForPrint(deck);
       applyGlobalStyles(deck);
       addLogoImage(deck);
+      tweakSlideNumber(deck);
       addFooter(deck);
       addChalkboardButtons(deck);
       handleTabbyClicks();

course-info/final-projects.qmd

@@ -29,7 +29,7 @@ cloud project.
 
 -   Projects are choose your own adventure:
 
-    1.  The [resource documents](resources/block-dna-resources.qmd)
+    1.  The [resource documents](/resources/block-dna-resources.qmd)
         contain data sets in from human S. cerevisiae. For example,
         sub-nucleosomal fragments provide a DNA-based signal to
         understand chromatin transactions that lead to transcription.

index.qmd

@@ -18,7 +18,6 @@ This page contains an outline of the topics, content, and assignments for the se
 #| echo: false
 #| message: false
 #| warning: false
-#| column: screen-inset-right
 library(tidyverse)
 library(fs)
 library(glue)
@@ -67,34 +66,39 @@ sched_tbl <- read_tsv(here("data/syllabus.tsv")) |>
     # set up links
     prepare_link = case_when(
       qmd_exists(prepare_html) == TRUE ~ glue('[{emo::ji("book")}]({prepare_html})'),
-      .default = ''
+      .default = '.'
     ),
     prepare_link = map(prepare_link, gt::md),
     slides_link = case_when(
       qmd_exists(slides_html) == TRUE ~ glue('[{emo::ji("page")}]({slides_html})'),
-      .default = ''
+      .default = '.'
     ),
     slides_link = map(slides_link, gt::md),
     # exercises links
     ex_link = case_when(
       qmd_exists(ex_html) == TRUE ~ glue('[{emo::ji("biceps")}]({ex_html})'),
-      .default = ''
+      .default = '.'
     ),
     ex_link = map(ex_link, gt::md),
     # problem sets links
     hw_link = case_when(
       qmd_exists(hw_html) == TRUE ~ glue('[{emo::ji("brain")}]({hw_html})'),
-      .default = ''
+      .default = '.'
     ),
     hw_link = map(hw_link, gt::md),
     # problem set keys links
     hw_key_link = case_when(
       qmd_exists(hw_key_html) == TRUE ~ glue('[{emo::ji("key")}]({hw_key_html})'),
-      .default = ''
+      .default = '.'
     ),
     hw_key_link = map(hw_key_link, gt::md)
   )
+```
 
+```{r}
+#| label: render-table
+#| echo: false
+#| column: screen-inset-right
 gt(
   sched_tbl,
   groupname_col = "week",
@@ -151,6 +155,5 @@ gt(
   opt_row_striping() |>
   cols_align(
     align = "center"
-  )
-
+  ) 
 ```