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kevinrue committed Oct 7, 2024
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107 changes: 106 additions & 1 deletion panels.html
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Expand Down Expand Up @@ -155,6 +189,10 @@ <h2 id="toc-title">On this page</h2>
<li><a href="#maplot" id="toc-maplot" class="nav-link" data-scroll-target="#maplot">MAPlot</a></li>
<li><a href="#volcanoplot" id="toc-volcanoplot" class="nav-link" data-scroll-target="#volcanoplot">VolcanoPlot</a></li>
</ul></li>
<li><a href="#iseehex" id="toc-iseehex" class="nav-link" data-scroll-target="#iseehex">iSEEhex</a>
<ul class="collapse">
<li><a href="#reduceddimensionhexplot" id="toc-reduceddimensionhexplot" class="nav-link" data-scroll-target="#reduceddimensionhexplot">ReducedDimensionHexPlot</a></li>
</ul></li>
</ul>
</nav>
</div>
Expand All @@ -178,7 +216,10 @@ <h1 class="title">Panels</h1>

</header>

<p>This page lists panels implemented in <a href="https://bioconductor.org/packages/iSEE/">iSEE</a> and its known extensions.</p>
<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>
<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 <em>almost</em> does what you would have in mind, then there is are options to make it do <em>exactly</em> that. Otherwise, options can be added, and more panel classes can be created, contact us!</p>
<section id="isee" class="level2">
<h2 class="anchored" data-anchor-id="isee">iSEE</h2>
<section id="columndataplot" class="level3">
Expand All @@ -190,6 +231,57 @@ <h3 class="anchored" data-anchor-id="columndataplot">ColumnDataPlot</h3>
<figcaption class="figure-caption">The <code>ColumnDataPlot</code> panel class.</figcaption>
</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-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-title-container flex-fill">
Expand To Reveal Code
</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 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>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(scRNAseq)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co"># Example data ----</span></span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>sce <span class="ot">&lt;-</span> <span class="fu">ReprocessedAllenData</span>(<span class="at">assays=</span><span class="st">"tophat_counts"</span>)</span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(scater)</span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>sce <span class="ot">&lt;-</span> <span class="fu">logNormCounts</span>(sce, <span class="at">exprs_values=</span><span class="st">"tophat_counts"</span>)</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a>sce <span class="ot">&lt;-</span> <span class="fu">runPCA</span>(sce, <span class="at">ncomponents=</span><span class="dv">4</span>)</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a>sce <span class="ot">&lt;-</span> <span class="fu">runTSNE</span>(sce)</span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a>sce <span class="ot">&lt;-</span> <span class="fu">runUMAP</span>(sce)</span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="fu">rowData</span>(sce)<span class="sc">$</span>ave_count <span class="ot">&lt;-</span> <span class="fu">rowMeans</span>(<span class="fu">assay</span>(sce, <span class="st">"tophat_counts"</span>))</span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="fu">rowData</span>(sce)<span class="sc">$</span>n_cells <span class="ot">&lt;-</span> <span class="fu">rowSums</span>(<span class="fu">assay</span>(sce, <span class="st">"tophat_counts"</span>) <span class="sc">&gt;</span> <span class="dv">0</span>)</span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a><span class="co"># launch the app itself ----</span></span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a>app <span class="ot">&lt;-</span> <span class="fu">iSEE</span>(sce, <span class="at">initial =</span> <span class="fu">list</span>(</span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a> <span class="fu">ColumnDataPlot</span>(</span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a> <span class="at">PanelWidth =</span> 8L,</span>
<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a> <span class="at">YAxis =</span> <span class="st">"NREADS"</span>,</span>
<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a> <span class="at">XAxis =</span> <span class="st">"Column data"</span>,</span>
<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a> <span class="at">XAxisColumnData =</span> <span class="st">"driver_1_s"</span>,</span>
<span id="cb1-25"><a href="#cb1-25" aria-hidden="true" tabindex="-1"></a> <span class="at">ColorBy =</span> <span class="st">"Column data"</span>,</span>
<span id="cb1-26"><a href="#cb1-26" aria-hidden="true" tabindex="-1"></a> <span class="at">ColorByColumnData =</span> <span class="st">"driver_1_s"</span>,</span>
<span id="cb1-27"><a href="#cb1-27" aria-hidden="true" tabindex="-1"></a> <span class="at">FacetColumnBy =</span> <span class="st">"Column data"</span>,</span>
<span id="cb1-28"><a href="#cb1-28" aria-hidden="true" tabindex="-1"></a> <span class="at">FacetColumnByColData =</span> <span class="st">"Core.Type"</span></span>
<span id="cb1-29"><a href="#cb1-29" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb1-30"><a href="#cb1-30" aria-hidden="true" tabindex="-1"></a>))</span>
<span id="cb1-31"><a href="#cb1-31" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-32"><a href="#cb1-32" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="fu">interactive</span>()) {</span>
<span id="cb1-33"><a href="#cb1-33" aria-hidden="true" tabindex="-1"></a> shiny<span class="sc">::</span><span class="fu">runApp</span>(app, <span class="at">port=</span><span class="dv">1234</span>)</span>
<span id="cb1-34"><a href="#cb1-34" 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>
</div>
</div>
</div>
</section>
<section id="columndatatable" class="level3">
<h3 class="anchored" data-anchor-id="columndatatable">ColumnDataTable</h3>
Expand Down Expand Up @@ -303,6 +395,19 @@ <h3 class="anchored" data-anchor-id="volcanoplot">VolcanoPlot</h3>
<figcaption class="figure-caption">The <code>VolcanoPlot</code> panel class.</figcaption>
</figure>
</div>
</section>
</section>
<section id="iseehex" class="level2">
<h2 class="anchored" data-anchor-id="iseehex">iSEEhex</h2>
<section id="reduceddimensionhexplot" class="level3">
<h3 class="anchored" data-anchor-id="reduceddimensionhexplot">ReducedDimensionHexPlot</h3>
<p>Same as <a href="#reduceddimensionplot"><code>ReducedDimensionPlot</code></a> but summarised using hexagonal bins.</p>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="images/panels/iSEEhex/ReducedDimensionHexPlot.png" class="img-fluid figure-img"></p>
<figcaption class="figure-caption">The <code>ReducedDimensionHexPlot</code> panel class.</figcaption>
</figure>
</div>
<!-- Links -->


Expand Down
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Expand Up @@ -205,7 +205,7 @@ <h2 class="anchored" data-anchor-id="bioconductor-pages">Bioconductor pages</h2>
</div>
</div>
<div class="callout-body-container callout-body">
<p>The links below redirect either to the latest version of each package on the <em>release</em> branch if available, or the latest version on the <em>development</em> branch for recent package that have are not distributed on a <em>release</em> branch yet. For more information, see <a href="https://www.bioconductor.org/install/">Using Bioconductor</a>.</p>
<p>The links below redirect either to the latest version of each package on the <em>release</em> branch if available, or the latest version on the <em>development</em> branch for recent package that have are not reached a <em>release</em> branch yet. For more information, see <a href="https://www.bioconductor.org/install/">Using Bioconductor</a>.</p>
</div>
</div>
<div class="quarto-layout-panel">
Expand Down Expand Up @@ -257,7 +257,7 @@ <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.</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 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>
</div>
</div>
<div class="quarto-layout-panel">
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