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install.html

@@ -206,28 +206,37 @@ <h2 class="anchored" data-anchor-id="install-fa-brands-r-project">Install <i cla
 </section>
 <section id="install-isee" class="level2">
 <h2 class="anchored" data-anchor-id="install-isee">Install iSEE</h2>
-<p>To install <em>iSEE</em>, start R and enter:</p>
-<div class="cell">
-<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">require</span>(<span class="st">"BiocManager"</span>, <span class="at">quietly =</span> <span class="cn">TRUE</span>))</span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>    <span class="fu">install.packages</span>(<span class="st">"BiocManager"</span>)</span>
-<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>BiocManager<span class="sc">::</span><span class="fu">install</span>(<span class="st">"iSEE"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<p>We recommend installing <em>iSEE</em> from the Bioconductor repository. The Bioconductor installation process will install the appropriate version of <em>iSEE</em> for your version of R.</p>
+<p><a href="https://bioconductor.org/packages/iSEE/">Install iSEE from Bioconductor</a></p>
+<div class="callout callout-style-default callout-note callout-titled">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-title-container flex-fill">
+Note
+</div>
+</div>
+<div class="callout-body-container callout-body">
+<p>Follow the link above and scroll down to the section <em>Installation</em>.</p>
+</div>
 </div>
-<p>Source: <a href="https://bioconductor.org/packages/iSEE/" class="uri">https://bioconductor.org/packages/iSEE/</a></p>
 </section>
 <section id="install-the-isee-verse" class="level2">
 <h2 class="anchored" data-anchor-id="install-the-isee-verse">Install the iSEE-verse</h2>
-<p>Install all known <em>iSEE</em> extensions packages with</p>
+<p>Most users do not need the full collection of packages that provide extensions to <em>iSEE</em>.</p>
+<p>For the aficionados, the command below does just that; it combines all the known <em>iSEE</em> extension packages into a single command that installs them all in one go.</p>
+<p>Great for copy-pasting, and for our <a href="https://bioconductor.org/packages/stats/bioc/iSEE/">download statistics</a>!</p>
 <div class="cell">
-<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>BiocManager<span class="sc">::</span><span class="fu">install</span>(<span class="fu">c</span>(</span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEE"</span>,</span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEde"</span>,</span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEhex"</span>,</span>
-<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEhub"</span>,</span>
-<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEindex"</span>,</span>
-<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEpathways"</span>,</span>
-<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEu"</span></span>
-<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>BiocManager<span class="sc">::</span><span class="fu">install</span>(<span class="fu">c</span>(</span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEde"</span>,</span>
+<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEhex"</span>,</span>
+<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEhub"</span>,</span>
+<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEindex"</span>,</span>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEpathways"</span>,</span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEtree"</span>,</span>
+<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a>    <span class="st">"iSEEu"</span></span>
+<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 
 

panels.html

@@ -219,7 +219,19 @@ <h1 class="title">Panels</h1>
 <p>This page showcases panels implemented in <a href="https://bioconductor.org/packages/iSEE/">iSEE</a> and its known extensions.</p>
 <p>Panels are grouped by package in which their are implemented (see the floating table of contents on the right).</p>
 <p>Each panel is introduced by a brief description above a single screenshot that illustrates a representative output, and the code used to produce that particular panel output in a live app.</p>
+<div class="callout callout-style-default callout-note callout-titled">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-title-container flex-fill">
+Note
+</div>
+</div>
+<div class="callout-body-container callout-body">
 <p>Bear in mind that all those panel classes come with many options to alter their respective outputs. This gallery showcases only a fraction of what each of those panels can do. In all likelihood, if a panel seems to do <em>almost</em> what you have in mind, then there are options to make it do <em>exactly</em> that. Otherwise, options can be added, and more panel classes can be created; check out our <a href="./resources.html">resources</a> to learn how!</p>
+</div>
+</div>
 <section id="isee" class="level2">
 <h2 class="anchored" data-anchor-id="isee">iSEE</h2>
 <section id="columndataplot" class="level3">
@@ -232,16 +244,16 @@ <h3 class="anchored" data-anchor-id="columndataplot">ColumnDataPlot</h3>
 </figure>
 </div>
 <div class="callout callout-style-default callout-caution callout-titled">
-<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-1-contents" aria-controls="callout-1" aria-expanded="false" aria-label="Toggle callout">
+<div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-2-contents" aria-controls="callout-2" aria-expanded="false" aria-label="Toggle callout">
 <div class="callout-icon-container">
 <i class="callout-icon"></i>
 </div>
 <div class="callout-title-container flex-fill">
-Expand To Reveal Code
+Reproduce This Output
 </div>
 <div class="callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end"><i class="callout-toggle"></i></div>
 </div>
-<div id="callout-1" class="callout-1-contents callout-collapse collapse">
+<div id="callout-2" class="callout-2-contents callout-collapse collapse">
 <div class="callout-body-container callout-body">
 <div class="cell">
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(iSEE)</span>

resources.html

@@ -153,7 +153,7 @@ <h2 id="toc-title">On this page</h2>
   </ul></li>
   <li><a href="#books" id="toc-books" class="nav-link" data-scroll-target="#books">Books</a>
   <ul class="collapse">
-  <li><a href="#iseethebook" id="toc-iseethebook" class="nav-link" data-scroll-target="#iseethebook">iSEETheBook</a></li>
+  <li><a href="#isee-the-book" id="toc-isee-the-book" class="nav-link" data-scroll-target="#isee-the-book">iSEE The Book</a></li>
   <li><a href="#extending-isee" id="toc-extending-isee" class="nav-link" data-scroll-target="#extending-isee">Extending iSEE</a></li>
   </ul></li>
   <li><a href="#videos" id="toc-videos" class="nav-link" data-scroll-target="#videos">Videos</a></li>
@@ -258,7 +258,7 @@ <h2 class="anchored" data-anchor-id="pkgdown-websites">pkgdown websites</h2>
 </div>
 </div>
 <div class="callout-body-container callout-body">
-<p>The latest version pushed to GitHub may be <em>ahead</em> of the latest version available on Bioconductor. As such, the documentation displayed in these websites may not be correspond to the version of packages that you are using. In doubt, always refer to help pages that you open in your own R session, using <code>?</code> or <code>help()</code>.</p>
+<p>The latest version pushed to GitHub may be <em>ahead</em> of the latest version available on Bioconductor. As such, the documentation displayed in these websites may not correspond to the version of packages that you are using. In doubt, always refer to help pages that you open in your own R session, using <code>?</code> or <code>help()</code>.</p>
 </div>
 </div>
 <div class="quarto-layout-panel">
@@ -325,13 +325,13 @@ <h3 class="anchored" data-anchor-id="bioconductor-conference-2019-workshop">Bioc
 </section>
 <section id="books" class="level2">
 <h2 class="anchored" data-anchor-id="books">Books</h2>
-<section id="iseethebook" class="level3">
-<h3 class="anchored" data-anchor-id="iseethebook">iSEETheBook</h3>
+<section id="isee-the-book" class="level3">
+<h3 class="anchored" data-anchor-id="isee-the-book">iSEE The Book</h3>
 <p><i class="fa-solid fa-book" aria-label="book"></i> <a href="https://isee.github.io/iSEETheBook/" class="uri">https://isee.github.io/iSEETheBook/</a></p>
 <p>This new book (work in progress) aims to compile essential knowledge about <em>iSEE</em>, catering for three main groups of users:</p>
 <ul>
 <li>End users interacting with the graphical user interface in their web browser.</li>
-<li>Developers of scripted web-applications using <em>iSEE</em> to showcase data sets.</li>
+<li>Developers of web-applications using <em>iSEE</em> to showcase data sets.</li>
 <li>Developers of extensions contributing new functionality and packages to the <em>iSEE</em> ecosystem.</li>
 </ul>
 </section>