wrap up

slides/lesson6_slides.html

@@ -8,7 +8,7 @@
 <link href="lesson6_slides_files/libs/quarto-html/light-border.css" rel="stylesheet">
 <link href="lesson6_slides_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
 <link href="lesson6_slides_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
-  <meta name="generator" content="quarto-1.3.353">
+  <meta name="generator" content="quarto-1.5.57">
 
   <title>Final class</title>
   <meta name="apple-mobile-web-app-capable" content="yes">
@@ -155,7 +155,8 @@
   }
 
   .callout.callout-titled .callout-body > .callout-content > :last-child {
-    margin-bottom: 0.5rem;
+    padding-bottom: 0.5rem;
+    margin-bottom: 0;
   }
 
   .callout.callout-titled .callout-icon::before {
@@ -353,17 +354,16 @@ <h2>In 6 weeks we have learned…</h2>
 </ul>
 </div>
 </section>
+<section id="cheatsheet" class="slide level2">
+<h2>Cheatsheet</h2>
+<p><a href="https://hutchdatascience.org/Intermediate_R/cheatsheet.html" class="uri">https://hutchdatascience.org/Intermediate_R/cheatsheet.html</a></p>
+</section>
 <section id="continuing-your-education" class="slide level2">
 <h2>Continuing your education</h2>
 <ul>
-<li>Advanced R</li>
-</ul>
-<div class="fragment">
-<ul>
-<li><a href="https://hutchdatascience.org/usergroups/">R Users Group</a></li>
+<li><a href="https://ocdo.fredhutch.org/dasl/courses/bioconductor/">Bioconductor for Genomics course in the Spring</a></li>
 </ul>
-</div>
-<div class="fragment">
+<!-- -->
 <ul>
 <li><p>Reference texts:</p>
 <ul>
@@ -372,23 +372,28 @@ <h2>Continuing your education</h2>
 <li><p><a href="https://r-graphics.org/">R Graphics Cookbook, by Winston Chang</a></p></li>
 </ul></li>
 </ul>
-</div>
 </section>
 <section id="connecting-to-rest-of-dasl" class="slide level2">
 <h2>Connecting to rest of DaSL…</h2>
-
-<img data-src="images/dasl_outreach.png" class="r-stretch"></section>
+<ul>
+<li><p><a href="https://ocdo.fredhutch.org/programs/dhc.html">Data House Calls</a></p></li>
+<li><p><a href="https://forms.office.com/r/YPxrxaw421">Building Computational Workflows Workshop, March 11 at noon</a></p></li>
+</ul>
+</section>
+<section id="certification" class="slide level2">
+<h2>Certification</h2>
+<p>You need to complete 4 out of 5 exercises - I’ll been keeping track <a href="https://docs.google.com/spreadsheets/d/1v2eMrqTt6aiXurwklSODzrMqagziAcU8TEeeJauYryU/edit?gid=0#gid=0">here</a>.</p>
+</section>
 <section id="please-fill-out-survey" class="slide level2">
 <h2>Please fill out survey!</h2>
-<p>Our <a href="https://forms.gle/DWH6WTe7o6nzhgHW7">class survey</a> makes a huge difference for us.</p>
+<p>Our <a href="https://forms.gle/Hc82MVnswsisXqot5">class survey</a> makes a huge difference for us.</p>
 </section>
-<section id="last-but-not-leaststickers" class="slide level2">
-<h2>Last but not least…stickers!</h2>
-<p><img data-src="https://2953482177-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-M38c0s4s0YCM6dGwrz1%2F-M7RetZBh2Wf7TnfLhKs%2F-M7RkjP-fqIgI8ZsDmKh%2Ftidyverse2.png?alt=media&amp;token=73bf5842-1ae0-4ca4-8622-ec2ae9063a7a" width="350"> <img data-src="images/Intro_To_R_2.png" width="350"></p>
-<p><img data-src="images/Intermediate_R_V3.png" width="350"><img data-src="images/student_stickers.jpg" width="350"></p>
-<p>Make your own sticker, add it to the wall of DaSL students!</p>
+<section id="section" class="slide level2">
+<h2></h2>
+<div class="quarto-auto-generated-content">
 <div class="footer footer-default">
 
+</div>
 </div>
 </section>
     </div>
@@ -417,7 +422,6 @@ <h2>Last but not least…stickers!</h2>
       Reveal.initialize({
 'controlsAuto': true,
 'previewLinksAuto': false,
-'smaller': true,
 'pdfSeparateFragments': false,
 'autoAnimateEasing': "ease",
 'autoAnimateDuration': 1,
@@ -634,18 +638,7 @@ <h2>Last but not least…stickers!</h2>
         }
         return false;
       }
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-          const codeEl = trigger.previousElementSibling.cloneNode(true);
-          for (const childEl of codeEl.children) {
-            if (isCodeAnnotation(childEl)) {
-              childEl.remove();
-            }
-          }
-          return codeEl.innerText;
-        }
-      });
-      clipboard.on('success', function(e) {
+      const onCopySuccess = function(e) {
         // button target
         const button = e.trigger;
         // don't keep focus
@@ -677,11 +670,50 @@ <h2>Last but not least…stickers!</h2>
         }, 1000);
         // clear code selection
         e.clearSelection();
+      }
+      const getTextToCopy = function(trigger) {
+          const codeEl = trigger.previousElementSibling.cloneNode(true);
+          for (const childEl of codeEl.children) {
+            if (isCodeAnnotation(childEl)) {
+              childEl.remove();
+            }
+          }
+          return codeEl.innerText;
+      }
+      const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
+        text: getTextToCopy
       });
-      function tippyHover(el, contentFn) {
+      clipboard.on('success', onCopySuccess);
+      if (window.document.getElementById('quarto-embedded-source-code-modal')) {
+        // For code content inside modals, clipBoardJS needs to be initialized with a container option
+        // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
+        const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
+          text: getTextToCopy,
+          container: window.document.getElementById('quarto-embedded-source-code-modal')
+        });
+        clipboardModal.on('success', onCopySuccess);
+      }
+        var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
+        var mailtoRegex = new RegExp(/^mailto:/);
+          var filterRegex = new RegExp('/' + window.location.host + '/');
+        var isInternal = (href) => {
+            return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
+        }
+        // Inspect non-navigation links and adorn them if external
+     	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
+        for (var i=0; i<links.length; i++) {
+          const link = links[i];
+          if (!isInternal(link.href)) {
+            // undo the damage that might have been done by quarto-nav.js in the case of
+            // links that we want to consider external
+            if (link.dataset.originalHref !== undefined) {
+              link.href = link.dataset.originalHref;
+            }
+          }
+        }
+      function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
         const config = {
           allowHTML: true,
-          content: contentFn,
           maxWidth: 500,
           delay: 100,
           arrow: false,
@@ -691,8 +723,17 @@ <h2>Last but not least…stickers!</h2>
           interactive: true,
           interactiveBorder: 10,
           theme: 'light-border',
-          placement: 'bottom-start'
+          placement: 'bottom-start',
         };
+        if (contentFn) {
+          config.content = contentFn;
+        }
+        if (onTriggerFn) {
+          config.onTrigger = onTriggerFn;
+        }
+        if (onUntriggerFn) {
+          config.onUntrigger = onUntriggerFn;
+        }
           config['offset'] = [0,0];
           config['maxWidth'] = 700;
         window.tippy(el, config); 
@@ -706,7 +747,11 @@ <h2>Last but not least…stickers!</h2>
           try { href = new URL(href).hash; } catch {}
           const id = href.replace(/^#\/?/, "");
           const note = window.document.getElementById(id);
-          return note.innerHTML;
+          if (note) {
+            return note.innerHTML;
+          } else {
+            return "";
+          }
         });
       }
       const findCites = (el) => {

slides/lesson6_slides.qmd

@@ -23,6 +23,8 @@ format:
 
 ## Cheatsheet
 
+<https://hutchdatascience.org/Intermediate_R/cheatsheet.html>
+
 ## Continuing your education
 
 -   [Bioconductor for Genomics course in the Spring](https://ocdo.fredhutch.org/dasl/courses/bioconductor/)
@@ -44,6 +46,10 @@ format:
 
 -   [Building Computational Workflows Workshop, March 11 at noon](https://forms.office.com/r/YPxrxaw421)
 
+## Certification
+
+You need to complete 4 out of 5 exercises - I'll been keeping track [here](https://docs.google.com/spreadsheets/d/1v2eMrqTt6aiXurwklSODzrMqagziAcU8TEeeJauYryU/edit?gid=0#gid=0).
+
 ## Please fill out survey!
 
 Our [class survey](https://forms.gle/Hc82MVnswsisXqot5) makes a huge difference for us.

slides/lesson6_slides_files/libs/quarto-html/quarto-html.min.css

@@ -1 +1 @@
-/*# sourceMappingURL=0a6b880beb84f9b6f36107a76f82c5b1.css.map */
+

slides/lesson6_slides_files/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 + ")"
             )
           );
         }

slides/lesson6_slides_files/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)
           }
         });
       }
@@ -272,6 +301,23 @@ window.QuartoSupport = function () {
     }
   }
 
+  function handleWhiteSpaceInColumns(deck) {
+    for (const outerDiv of window.document.querySelectorAll("div.columns")) {
+      // remove all whitespace text nodes
+      // whitespace nodes cause the columns to be misaligned
+      // since they have inline-block layout
+      // 
+      // Quarto emits no whitespace nodes, but third-party tooling
+      // has bugs that can cause whitespace nodes to be emitted.
+      // See https://github.com/quarto-dev/quarto-cli/issues/8382
+      for (const node of outerDiv.childNodes) {
+        if (node.nodeType === 3 && node.nodeValue.trim() === "") {
+          outerDiv.removeChild(node);
+        }
+      }
+    }
+  }
+
   return {
     id: "quarto-support",
     init: function (deck) {
@@ -280,11 +326,13 @@ window.QuartoSupport = function () {
       fixupForPrint(deck);
       applyGlobalStyles(deck);
       addLogoImage(deck);
+      tweakSlideNumber(deck);
       addFooter(deck);
       addChalkboardButtons(deck);
       handleTabbyClicks();
       handleSlideChanges(deck);
       workaroundMermaidDistance(deck);
+      handleWhiteSpaceInColumns(deck);
     },
   };
 };