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<h1 class="title"><span id="sec-a5" class="quarto-section-identifier">Appendix E — YAML Parameters</span></h1>
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<p>All reports are run from a <code>Parent.qmd</code> file, which has a yaml header with a <code>params</code> section.</p>
<p>The various parameters of this section are described below.</p>
<section id="explanation-of-yaml-parameters" class="level2" data-number="E.1">
<h2 data-number="E.1" class="anchored" data-anchor-id="explanation-of-yaml-parameters"><span class="header-section-number">E.1</span> Explanation of YAML Parameters</h2>
<table class="table">
<colgroup>
<col style="width: 22%">
<col style="width: 13%">
<col style="width: 63%">
</colgroup>
<thead>
<tr class="header">
<th style="text-align: center;">Parameter</th>
<th style="text-align: center;">Default Value</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: center;"><code>adcode</code></td>
<td style="text-align: center;"><code>false</code></td>
<td>Whether to show R code.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>analyse_type</code></td>
<td style="text-align: center;"><p><code>null</code></p>
<p><code><QC,DA,DS></code></p></td>
<td>Specify analysis type.</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>annotation_column</code></td>
<td style="text-align: center;"><code>null</code></td>
<td>Column used for annotation; defaults to none.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>batch</code></td>
<td style="text-align: center;"><code>null</code></td>
<td>Batch metadata column name for the analysis, if applicable.</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>cluster_id</code></td>
<td style="text-align: center;"><code>"cluster_id"</code></td>
<td>Default identifier for clusters.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>col_block</code></td>
<td style="text-align: center;"><code>null</code></td>
<td><code>block_id</code>’s diffcyt parameter.</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>cols_design_GLMM_random</code></td>
<td style="text-align: center;"><code>null</code></td>
<td>Columns used in GLMM for random effects.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>conditions</code></td>
<td style="text-align: center;"><code>null</code></td>
<td>Conditions metadata column name under which the analysis is performed.</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>conditions_reference</code></td>
<td style="text-align: center;"><code>null</code></td>
<td>Reference condition for comparison in analyses.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>contrast</code></td>
<td style="text-align: center;"><code>null</code></td>
<td>Contrast condition for analysis, each is compare to <code>conditions_reference</code> .</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>fc</code></td>
<td style="text-align: center;"><code>1</code></td>
<td>Fold change threshold for significance.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>log_bar</code></td>
<td style="text-align: center;"><code>false</code></td>
<td>Whether to use logarithmic scaling on bar plots.</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>min_cells</code></td>
<td style="text-align: center;"><code>1</code></td>
<td>Minimum number of cells required per sample.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>min_samples</code></td>
<td style="text-align: center;"><code>null</code></td>
<td>Minimum number of samples required for analysis.</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>path</code></td>
<td style="text-align: center;"><code><file path></code></td>
<td>Path to the data file.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>p_value</code></td>
<td style="text-align: center;"><code>0.05</code></td>
<td>P-value threshold for statistical significance.</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>plot_legends</code></td>
<td style="text-align: center;"><code>null</code></td>
<td>Metadata column name to add on graphs.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>project</code></td>
<td style="text-align: center;"><code>null</code></td>
<td>Project description if provided.</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>rds</code></td>
<td style="text-align: center;"><code><.rds></code></td>
<td>RDS file name.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>show_parameters</code></td>
<td style="text-align: center;"><code>true</code></td>
<td>Whether to show parameters in outputs.</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>show_summary</code></td>
<td style="text-align: center;"><code>true</code></td>
<td>Whether to display summary information tables.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>show_heatmap_on_off</code></td>
<td style="text-align: center;"><code>true</code></td>
<td>Whether to show or hide the number of cells per fcs heatmaps.</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>sorted</code></td>
<td style="text-align: center;"><code>false</code></td>
<td>Whether data should be sorted on graph by <code>conditions</code>.</td>
</tr>
<tr class="even">
<td style="text-align: center;"><code>transform</code></td>
<td style="text-align: center;"><code>false</code></td>
<td>Whether data should be transformed on Differential analysis.</td>
</tr>
<tr class="odd">
<td style="text-align: center;"><code>subset_column</code></td>
<td style="text-align: center;"><code>null</code></td>
<td>Column used for subsetting data, if applicable.</td>
</tr>
</tbody>
</table>
</section>
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const stylesheet = stylesheets[i];
stylesheet.rel = 'stylesheet';
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const els = window.document.querySelectorAll(selector);
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const el = els[i];
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el.classList.add('notransition');
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const alternateTheme = document.querySelector('#giscus-alt-theme')?.value ?? 'dark';
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newTheme = isAlternate ? alternateTheme : baseTheme;
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const changeGiscusTheme = () => {
// From: https://github.com/giscus/giscus/issues/336
const sendMessage = (message) => {
const iframe = document.querySelector('iframe.giscus-frame');
if (!iframe) return;
iframe.contentWindow.postMessage({ giscus: message }, 'https://giscus.app');
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sendMessage({
setConfig: {
theme: newTheme
}
});
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const isGiscussLoaded = window.document.querySelector('iframe.giscus-frame') !== null;
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changeGiscusTheme();
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const toggleColorMode = (alternate) => {
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manageTransitions('#quarto-margin-sidebar .nav-link', false);
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if (navigator.userAgent.indexOf('Safari') > 0 && navigator.userAgent.indexOf('Chrome') == -1) {
manageTransitions("body", false);
window.scrollTo(0, 1);
setTimeout(() => {
window.scrollTo(0, 0);
manageTransitions("body", true);
}, 40);
}
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const storageValue = window.localStorage.getItem("quarto-color-scheme");
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return localAlternateSentinel;
}
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let toAlternate = !hasAlternateSentinel();
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setStyleSentinel(toAlternate);
toggleGiscusIfUsed(toAlternate, darkModeDefault);
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const a = window.document.createElement('a');
a.classList.add('top-right');
a.classList.add('quarto-color-scheme-toggle');
a.href = "";
a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; };
const i = window.document.createElement("i");
i.classList.add('bi');
a.appendChild(i);
window.document.body.appendChild(a);
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anchorJS.add('.anchored');
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text: function(trigger) {
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return codeEl.innerText;
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button.setAttribute("title", "Copied!");
let tooltip;
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button.setAttribute("data-bs-toggle", "tooltip");
button.setAttribute("data-bs-placement", "left");
button.setAttribute("data-bs-title", "Copied!");
tooltip = new bootstrap.Tooltip(button,
{ trigger: "manual",
customClass: "code-copy-button-tooltip",
offset: [0, -8]});
tooltip.show();
}
setTimeout(function() {
if (tooltip) {
tooltip.hide();
button.removeAttribute("data-bs-title");
button.removeAttribute("data-bs-toggle");
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button.setAttribute("title", currentTitle);
button.classList.remove('code-copy-button-checked');
}, 1000);
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maxWidth: 500,
delay: 100,
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interactiveBorder: 10,
theme: 'quarto',
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config.onTrigger = onTriggerFn;
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const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
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return note.innerHTML;
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instance.disable();
let url = xref.getAttribute('href');
let hash = undefined;
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const id = hash.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
if (note !== null) {
try {
const html = processXRef(id, note);
instance.setContent(html);
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instance.enable();
instance.show();
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} 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);
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instance.enable();
instance.show();
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let cellAttr = 'data-code-cell="' + cell + '"';
let lineAttr = 'data-code-annotation="' + annotation + '"';
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return selector;
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const targetCell = annoteEl.getAttribute("data-target-cell");
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
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height = el.offsetHeight;
parent = el.parentElement.parentElement;
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parent.appendChild(div);
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const gutter = codeCell.querySelector('.code-annotation-gutter');
gutter.appendChild(gutterDiv);
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gutterDiv.style.top = top - 2 + "px";
gutterDiv.style.height = height + 4 + "px";
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selectedAnnoteEl = annoteEl;
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const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
elementsIds.forEach((elId) => {
const div = window.document.getElementById(elId);
if (div) {
div.remove();
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selectedAnnoteEl = undefined;
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selectCodeLines(clickedEl);
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const cites = parentEl.dataset.cites;
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el,
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};
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}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
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var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
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citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
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citeDiv.innerHTML = biblioDiv.innerHTML;
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popup.appendChild(citeDiv);
});
return popup.innerHTML;
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</script>
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