Day 1
Lecture 3 - R developer toolkit
Developing R/Bioconductor packages for Genomics
Welcome
Program
Prerequesites
Extra resources
Day 1
Lecture 0 - Introduction to the workshop
Lecture 1 - R package architecture
Lecture 2 - Introduction to Bioconductor
Lecture 3 - R developer toolkit
Day 2
Lecture 4 - Continuous development
Lecture 5 - Bioconductor 201
Day 3
Lecture 6 - Git versioning
Lecture 8 - Vignettes and data
Day 4
Lecture 7 - S4 classes in Bioconductor
Lecture 9 - Bioconductor package submission
Day 5
Lecture 10 - Other package types
Lecture 11 - Package dissemination
Exercises
1
Getting started with Bioconductor ecosystem
2
Kickstarting an R package
3
Enriching package functionalities
4
Using S4 classes in a package
5
Improving package integration
Lecture 3 - R developer toolkit
<div id="quarto-navigation-envelope" class="hidden"> <p><span class="hidden" data-render-id="quarto-int-sidebar-title">Developing R/Bioconductor packages for Genomics</span> <span class="hidden" data-render-id="quarto-int-navbar-title">Developing R/Bioconductor packages for Genomics</span> <span class="hidden" data-render-id="quarto-int-next">Lecture 4 - Continuous development</span> <span class="hidden" data-render-id="quarto-int-prev">Lecture 2 - Introduction to Bioconductor</span> <span class="hidden" data-render-id="quarto-int-sidebar:/index.html">Welcome</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/program.html">Program</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/prerequisites.html">Prerequesites</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/extra.html">Extra resources</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-1">Day 1</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture0_course-overview.html">Lecture 0 - Introduction to the workshop</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture1_Package_architecture.html">Lecture 1 - R package architecture</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture2_Bioconductor_101.html">Lecture 2 - Introduction to Bioconductor</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day1/Lecture3_Developer-toolkit.html">Lecture 3 - R developer toolkit</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-2">Day 2</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lecture4_Continuous_development-writing-documenting-testing.html">Lecture 4 - Continuous development</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day2/Lecture5_Bioconductor_201.html">Lecture 5 - Bioconductor 201</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-3">Day 3</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lecture6_Git_versionning.html">Lecture 6 - Git versioning</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day3/Lecture7_Improving_package-data_vignettes-....html">Lecture 8 - Vignettes and data</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-4">Day 4</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lecture8_S4_classes.html">Lecture 7 - S4 classes in Bioconductor</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day4/Lecture9_Bioconductor_submission.html">Lecture 9 - Bioconductor package submission</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-5">Day 5</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Lecture10_Other_package_types.html">Lecture 10 - Other package types</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/day5/Lecture11_Package_dissemination.html">Lecture 11 - Package dissemination</span> <span class="hidden" data-render-id="quarto-int-sidebar:quarto-sidebar-section-6">Exercises</span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/exercises/Day1_Getting-started-with-Bioc.html"><span class="chapter-number">1</span> <span class="chapter-title">Getting started with Bioconductor ecosystem</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/exercises/Day2_Developer-virtuous-circle.html"><span class="chapter-number">2</span> <span class="chapter-title">Kickstarting an R package</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/exercises/Day3_Examples-test-data.html"><span class="chapter-number">3</span> <span class="chapter-title">Enriching package functionalities</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/exercises/Day4_S4-classes.html"><span class="chapter-number">4</span> <span class="chapter-title">Using S4 classes in a package</span></span> <span class="hidden" data-render-id="quarto-int-sidebar:/content/exercises/Day5_package-integration.html"><span class="chapter-number">5</span> <span class="chapter-title">Improving package integration</span></span> <span class="hidden" data-render-id="footer-left">Developing R/Bioconductor packages for Genomics |<br /> J. Serizay</span> <span class="hidden" data-render-id="footer-right">This book was built with <a href="https://quarto.org/">Quarto</a>.</span> <span class="hidden" data-render-id="quarto-breadcrumbs-faba582bb439d5cd836a674b446052c1">Day 1</span> <span class="hidden" data-render-id="quarto-breadcrumbs-6750fe5f16f9220061a82844e4ff31e1">Lecture 3 - R developer toolkit</span></p> </div> <div id="quarto-meta-markdown" class="hidden"> <p><span class="hidden" data-render-id="quarto-metatitle">Developing R/Bioconductor packages for Genomics - Lecture 3 - R developer toolkit</span> <span class="hidden" data-render-id="quarto-twittercardtitle">Developing R/Bioconductor packages for Genomics - Lecture 3 - R developer toolkit</span> <span class="hidden" data-render-id="quarto-ogcardtitle">Developing R/Bioconductor packages for Genomics - Lecture 3 - R developer toolkit</span> <span class="hidden" data-render-id="quarto-metasitename">Developing R/Bioconductor packages for Genomics</span> <span class="hidden" data-render-id="quarto-twittercarddesc"></span> <span class="hidden" data-render-id="quarto-ogcardddesc"></span></p> </div> </main> <!-- /main --> <script id = "quarto-html-after-body" type="application/javascript"> window.document.addEventListener("DOMContentLoaded", function (event) { const toggleBodyColorMode = (bsSheetEl) => { const mode = bsSheetEl.getAttribute("data-mode"); const bodyEl = window.document.querySelector("body"); if (mode === "dark") { bodyEl.classList.add("quarto-dark"); bodyEl.classList.remove("quarto-light"); } else { bodyEl.classList.add("quarto-light"); bodyEl.classList.remove("quarto-dark"); } } const toggleBodyColorPrimary = () => { const bsSheetEl = window.document.querySelector("link#quarto-bootstrap"); if (bsSheetEl) { toggleBodyColorMode(bsSheetEl); } } toggleBodyColorPrimary(); const icon = ""; const anchorJS = new window.AnchorJS(); anchorJS.options = { placement: 'right', icon: icon }; anchorJS.add('.anchored'); const isCodeAnnotation = (el) => { for (const clz of el.classList) { if (clz.startsWith('code-annotation-')) { return true; } } return false; } const clipboard = new window.ClipboardJS('.code-copy-button', { 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) { // button target const button = e.trigger; // don't keep focus button.blur(); // flash "checked" button.classList.add('code-copy-button-checked'); var currentTitle = button.getAttribute("title"); button.setAttribute("title", "Copied!"); let tooltip; if (window.bootstrap) { 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"); button.removeAttribute("data-bs-placement"); } button.setAttribute("title", currentTitle); button.classList.remove('code-copy-button-checked'); }, 1000); // clear code selection e.clearSelection(); }); function tippyHover(el, contentFn) { const config = { allowHTML: true, content: contentFn, maxWidth: 500, delay: 100, arrow: false, appendTo: function(el) { return el.parentElement; }, interactive: true, interactiveBorder: 10, theme: 'quarto', placement: 'bottom-start' }; window.tippy(el, config); } const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]'); for (var i=0; i<noterefs.length; i++) { const ref = noterefs[i]; tippyHover(ref, function() { // use id or data attribute instead here let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href'); try { href = new URL(href).hash; } catch {} const id = href.replace(/^#\/?/, ""); const note = window.document.getElementById(id); return note.innerHTML; }); } let selectedAnnoteEl; const selectorForAnnotation = ( cell, annotation) => { let cellAttr = 'data-code-cell="' + cell + '"'; let lineAttr = 'data-code-annotation="' + annotation + '"'; const selector = 'span[' + cellAttr + '][' + lineAttr + ']'; return selector; } const selectCodeLines = (annoteEl) => { const doc = window.document; const targetCell = annoteEl.getAttribute("data-target-cell"); const targetAnnotation = annoteEl.getAttribute("data-target-annotation"); const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation)); const lines = annoteSpan.getAttribute("data-code-lines").split(","); const lineIds = lines.map((line) => { return targetCell + "-" + line; }) let top = null; let height = null; let parent = null; if (lineIds.length > 0) { //compute the position of the single el (top and bottom and make a div) const el = window.document.getElementById(lineIds[0]); top = el.offsetTop; height = el.offsetHeight; parent = el.parentElement.parentElement; if (lineIds.length > 1) { const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]); const bottom = lastEl.offsetTop + lastEl.offsetHeight; height = bottom - top; } if (top !== null && height !== null && parent !== null) { // cook up a div (if necessary) and position it let div = window.document.getElementById("code-annotation-line-highlight"); if (div === null) { div = window.document.createElement("div"); div.setAttribute("id", "code-annotation-line-highlight"); div.style.position = 'absolute'; parent.appendChild(div); } div.style.top = top - 2 + "px"; div.style.height = height + 4 + "px"; let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter"); if (gutterDiv === null) { gutterDiv = window.document.createElement("div"); gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter"); gutterDiv.style.position = 'absolute'; const codeCell = window.document.getElementById(targetCell); const gutter = codeCell.querySelector('.code-annotation-gutter'); gutter.appendChild(gutterDiv); } gutterDiv.style.top = top - 2 + "px"; gutterDiv.style.height = height + 4 + "px"; } selectedAnnoteEl = annoteEl; } }; const unselectCodeLines = () => { const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"]; elementsIds.forEach((elId) => { const div = window.document.getElementById(elId); if (div) { div.remove(); } }); selectedAnnoteEl = undefined; }; // Attach click handler to the DT const annoteDls = window.document.querySelectorAll('dt[data-target-cell]'); for (const annoteDlNode of annoteDls) { annoteDlNode.addEventListener('click', (event) => { const clickedEl = event.target; if (clickedEl !== selectedAnnoteEl) { unselectCodeLines(); const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active'); if (activeEl) { activeEl.classList.remove('code-annotation-active'); } selectCodeLines(clickedEl); clickedEl.classList.add('code-annotation-active'); } else { // Unselect the line unselectCodeLines(); clickedEl.classList.remove('code-annotation-active'); } }); } const findCites = (el) => { const parentEl = el.parentElement; if (parentEl) { const cites = parentEl.dataset.cites; if (cites) { return { el, cites: cites.split(' ') }; } else { return findCites(el.parentElement) } } else { return undefined; } }; var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]'); for (var i=0; i<bibliorefs.length; i++) { const ref = bibliorefs[i]; const citeInfo = findCites(ref); if (citeInfo) { tippyHover(citeInfo.el, function() { var popup = window.document.createElement('div'); citeInfo.cites.forEach(function(cite) { var citeDiv = window.document.createElement('div'); citeDiv.classList.add('hanging-indent'); citeDiv.classList.add('csl-entry'); var biblioDiv = window.document.getElementById('ref-' + cite); if (biblioDiv) { citeDiv.innerHTML = biblioDiv.innerHTML; } popup.appendChild(citeDiv); }); return popup.innerHTML; }); } } }); </script> <nav class="page-navigation"> <div class="nav-page nav-page-previous"> <a href="/content/day1/Lecture2_Bioconductor_101.html" class="pagination-link"> <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Lecture 2 - Introduction to Bioconductor</span> </a> </div> <div class="nav-page nav-page-next"> <a href="/content/day2/Lecture4_Continuous_development-writing-documenting-testing.html" class="pagination-link"> <span class="nav-page-text">Lecture 4 - Continuous development</span> <i class="bi bi-arrow-right-short"></i> </a> </div> </nav> </div> <!-- /content --> <footer class="footer"> <div class="nav-footer"> <div class="nav-footer-left"> <div class='footer-contents'>Developing R/Bioconductor packages for Genomics | J. Serizay </div> </div> <div class="nav-footer-center"> </div> <div class="nav-footer-right"> <div class='footer-contents'>This book was built with <a href="https://quarto.org/">Quarto</a>. </div> </div> </div> </footer> </body> </html>