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@TuomasBorman
TuomasBorman committed Nov 22, 2024
1 parent c984b10 commit 09fe294
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234 changes: 216 additions & 18 deletions docs/index.html
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<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-1.5.57">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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"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",
Expand All @@ -53,6 +59,7 @@
"search-more-match-text": "more match in this document",
"search-more-matches-text": "more matches in this document",
"search-clear-button-title": "Clear",
"search-text-placeholder": "",
"search-detached-cancel-button-title": "Cancel",
"search-submit-button-title": "Submit",
"search-label": "Search"
Expand Down Expand Up @@ -88,8 +95,10 @@ <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>
Expand All @@ -98,6 +107,7 @@ <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>
<li><a href="https://microbiome.github.io/outreach/oma.html" target="_blank">Orchestrating microbiome Analysis with Bioconductor</a></li>
</ul>
</section>
<section id="quarto" class="level3">
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}
return false;
}
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text: function(trigger) {
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
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}, 1000);
// clear code selection
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childEl.remove();
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}
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text: getTextToCopy
});
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clipboard.on('success', onCopySuccess);
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// 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);
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content: contentFn,
maxWidth: 500,
delay: 100,
arrow: false,
Expand All @@ -253,8 +291,17 @@ <h2 class="anchored" data-anchor-id="contributions">Contributions</h2>
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start'
placement: 'bottom-start',
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}
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window.tippy(el, config);
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const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
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try { href = new URL(href).hash; } catch {}
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return "";
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break;
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window.Quarto.typesetMath(container);
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window.Quarto.typesetMath(note);
}
return note.innerHTML;
}
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if (anchorLink) {
anchorLink.remove();
}
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(note);
}
// TODO in 1.5, we should make sure this works without a callout special case
if (note.classList.contains("callout")) {
return note.outerHTML;
} else {
return note.innerHTML;
}
}
}
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instance.disable();
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}
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const html = processXRef(id, note.cloneNode(true));
instance.setContent(html);
} finally {
instance.enable();
instance.show();
}
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fetch(url.split('#')[0])
.then(res => res.text())
.then(html => {
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const html = processXRef(id, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
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// 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();
}
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instance.setContent(html);
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instance.enable();
instance.show();
});
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}, function(instance) {
});
}
let selectedAnnoteEl;
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}
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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");
Expand All @@ -335,6 +506,32 @@ <h2 class="anchored" data-anchor-id="contributions">Contributions</h2>
});
selectedAnnoteEl = undefined;
};
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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) {
Expand Down Expand Up @@ -398,4 +595,5 @@ <h2 class="anchored" data-anchor-id="contributions">Contributions</h2>




</body></html>
4 changes: 2 additions & 2 deletions docs/search.json
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Expand Up @@ -81,14 +81,14 @@
"href": "index.html",
"title": "Quarto Presentations",
"section": "",
"text": "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:\n\n\n\nIntro\nBioconductor project\n\n\n\n\n\nReproducible workflow with Quarto\nLearning environment\nWorkflow\n\n\n\n\n\nMGnifyR: An R package for accessing MGnify microbiome data\n\n\n\n\n\nOrchestrating microbiome multi-omics with R & Bioconductor\nData containers\nSummarizedExperiment\nTreeSummarizedExperiment\n\n\n\n\n\nHintikkaXOData\nTengeler2020\n\n\n\n\n\nData Manipulation\nIntroduction to Quarto\nAlpha Diversity\nPCoA\ndbRDA\nCompositional Heatmaps\nDifferential Abundance\nDay 2"
"text": "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:\n\n\n\nIntro\nBioconductor project\nOrchestrating microbiome Analysis with Bioconductor\n\n\n\n\n\nReproducible workflow with Quarto\nLearning environment\nWorkflow\n\n\n\n\n\nMGnifyR: An R package for accessing MGnify microbiome data\n\n\n\n\n\nOrchestrating microbiome multi-omics with R & Bioconductor\nData containers\nSummarizedExperiment\nTreeSummarizedExperiment\n\n\n\n\n\nHintikkaXOData\nTengeler2020\n\n\n\n\n\nData Manipulation\nIntroduction to Quarto\nAlpha Diversity\nPCoA\ndbRDA\nCompositional Heatmaps\nDifferential Abundance\nDay 2"
},
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"href": "index.html#overview",
"title": "Quarto Presentations",
"section": "",
"text": "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:\n\n\n\nIntro\nBioconductor project\n\n\n\n\n\nReproducible workflow with Quarto\nLearning environment\nWorkflow\n\n\n\n\n\nMGnifyR: An R package for accessing MGnify microbiome data\n\n\n\n\n\nOrchestrating microbiome multi-omics with R & Bioconductor\nData containers\nSummarizedExperiment\nTreeSummarizedExperiment\n\n\n\n\n\nHintikkaXOData\nTengeler2020\n\n\n\n\n\nData Manipulation\nIntroduction to Quarto\nAlpha Diversity\nPCoA\ndbRDA\nCompositional Heatmaps\nDifferential Abundance\nDay 2"
"text": "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:\n\n\n\nIntro\nBioconductor project\nOrchestrating microbiome Analysis with Bioconductor\n\n\n\n\n\nReproducible workflow with Quarto\nLearning environment\nWorkflow\n\n\n\n\n\nMGnifyR: An R package for accessing MGnify microbiome data\n\n\n\n\n\nOrchestrating microbiome multi-omics with R & Bioconductor\nData containers\nSummarizedExperiment\nTreeSummarizedExperiment\n\n\n\n\n\nHintikkaXOData\nTengeler2020\n\n\n\n\n\nData Manipulation\nIntroduction to Quarto\nAlpha Diversity\nPCoA\ndbRDA\nCompositional Heatmaps\nDifferential Abundance\nDay 2"
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