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microbiome · Jul 8, 2024 · f50bae8 · f50bae8
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diff --git a/docs/images/tengeler_alpha.png b/docs/images/tengeler_alpha.png
diff --git a/docs/images/tengeler_beta.png b/docs/images/tengeler_beta.png
diff --git a/docs/images/tengeler_paper.png b/docs/images/tengeler_paper.png
diff --git a/docs/images/tengeler_timeline.png b/docs/images/tengeler_timeline.png
diff --git a/docs/images/turun_yliopiston_logo.jpg b/docs/images/turun_yliopiston_logo.jpg
diff --git a/docs/index.html b/docs/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.3.450">
+<meta name="generator" content="quarto-1.4.506">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -44,7 +44,13 @@
   "collapse-after": 3,
   "panel-placement": "start",
   "type": "textbox",
-  "limit": 20,
+  "limit": 50,
+  "keyboard-shortcut": [
+    "f",
+    "/",
+    "s"
+  ],
+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -88,14 +94,17 @@ <h1 class="title">Quarto Presentations</h1>
   </div>
 
 
+
 </header>
 
+
 <section id="overview" class="level2">
 <h2 class="anchored" data-anchor-id="overview">Overview</h2>
 <p>This website hosts quarto presentations about microbiome analysis and data integration with mia and other related packages. Our presentations were prepared for past courses and conferences and cover a broad range of topics in the scope of biological data science. Currently, you can find the following subjects:</p>
 <section id="bioconductor" class="level3">
 <h3 class="anchored" data-anchor-id="bioconductor">Bioconductor</h3>
 <ul>
+<li><a href="https://microbiome.github.io/outreach/intro.html" target="_blank">Intro</a></li>
 <li><a href="https://microbiome.github.io/outreach/bioconductor.html" target="_blank">Bioconductor project</a></li>
 </ul>
 </section>
@@ -232,10 +241,9 @@ <h2 class="anchored" data-anchor-id="contributions">Contributions</h2>
     // clear code selection
     e.clearSelection();
   });
-  function tippyHover(el, contentFn) {
+  function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
     const config = {
       allowHTML: true,
-      content: contentFn,
       maxWidth: 500,
       delay: 100,
       arrow: false,
@@ -245,8 +253,17 @@ <h2 class="anchored" data-anchor-id="contributions">Contributions</h2>
       interactive: true,
       interactiveBorder: 10,
       theme: 'quarto',
-      placement: 'bottom-start'
+      placement: 'bottom-start',
     };
+    if (contentFn) {
+      config.content = contentFn;
+    }
+    if (onTriggerFn) {
+      config.onTrigger = onTriggerFn;
+    }
+    if (onUntriggerFn) {
+      config.onUntrigger = onUntriggerFn;
+    }
     window.tippy(el, config); 
   }
   const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
@@ -260,6 +277,135 @@ <h2 class="anchored" data-anchor-id="contributions">Contributions</h2>
       const note = window.document.getElementById(id);
       return note.innerHTML;
     });
+  }
+  const xrefs = window.document.querySelectorAll('a.quarto-xref');
+  const processXRef = (id, note) => {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
+      // Special case sections, only their first couple elements
+      const container = document.createElement("div");
+      if (note.children && note.children.length > 2) {
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
+        }
+        typesetMath(container);
+        return container.innerHTML
+      } else {
+        typesetMath(note);
+        return note.innerHTML;
+      }
+    } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      typesetMath(note);
+      return note.innerHTML;
+    }
+  }
+  for (var i=0; i<xrefs.length; i++) {
+    const xref = xrefs[i];
+    tippyHover(xref, undefined, function(instance) {
+      instance.disable();
+      let url = xref.getAttribute('href');
+      let hash = undefined; 
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
+        }
+      } else {
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
+        .then(res => res.text())
+        .then(html => {
+          const parser = new DOMParser();
+          const htmlDoc = parser.parseFromString(html, "text/html");
+          const note = htmlDoc.querySelector('main.content');
+          if (note !== null) {
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
+            instance.setContent(html);
+          } 
+        }).finally(() => {
+          instance.enable();
+          instance.show();
+        });
+      }
+    }, function(instance) {
+    });
   }
       let selectedAnnoteEl;
       const selectorForAnnotation = ( cell, annotation) => {
@@ -302,6 +448,7 @@ <h2 class="anchored" data-anchor-id="contributions">Contributions</h2>
             }
             div.style.top = top - 2 + "px";
             div.style.height = height + 4 + "px";
+            div.style.left = 0;
             let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
             if (gutterDiv === null) {
               gutterDiv = window.document.createElement("div");
@@ -327,6 +474,32 @@ <h2 class="anchored" data-anchor-id="contributions">Contributions</h2>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -390,4 +563,5 @@ <h2 class="anchored" data-anchor-id="contributions">Contributions</h2>
 
 
 
+
 </body></html>