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404.html

@@ -186,7 +186,11 @@
 <ul>
 <li class="chapter" data-level="4.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#presentation-1"><i class="fa fa-check"></i><b>4.1</b> Presentation</a></li>
 <li class="chapter" data-level="4.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#ecosystem"><i class="fa fa-check"></i><b>4.2</b> Ecosystem</a></li>
-<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a></li>
+<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a>
+<ul>
+<li class="chapter" data-level="4.3.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-installation-1"><i class="fa fa-check"></i><b>4.3.1</b> Giotto installation</a></li>
+<li class="chapter" data-level="4.3.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#python-environment"><i class="fa fa-check"></i><b>4.3.2</b> Python environment</a></li>
+</ul></li>
 <li class="chapter" data-level="4.4" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-instructions"><i class="fa fa-check"></i><b>4.4</b> Giotto instructions</a></li>
 </ul></li>
 <li class="chapter" data-level="5" data-path="data-formatting-and-pre-processing.html"><a href="data-formatting-and-pre-processing.html"><i class="fa fa-check"></i><b>5</b> Data formatting and Pre-processing</a>

contributing-to-giotto.html

@@ -186,7 +186,11 @@
 <ul>
 <li class="chapter" data-level="4.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#presentation-1"><i class="fa fa-check"></i><b>4.1</b> Presentation</a></li>
 <li class="chapter" data-level="4.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#ecosystem"><i class="fa fa-check"></i><b>4.2</b> Ecosystem</a></li>
-<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a></li>
+<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a>
+<ul>
+<li class="chapter" data-level="4.3.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-installation-1"><i class="fa fa-check"></i><b>4.3.1</b> Giotto installation</a></li>
+<li class="chapter" data-level="4.3.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#python-environment"><i class="fa fa-check"></i><b>4.3.2</b> Python environment</a></li>
+</ul></li>
 <li class="chapter" data-level="4.4" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-instructions"><i class="fa fa-check"></i><b>4.4</b> Giotto instructions</a></li>
 </ul></li>
 <li class="chapter" data-level="5" data-path="data-formatting-and-pre-processing.html"><a href="data-formatting-and-pre-processing.html"><i class="fa fa-check"></i><b>5</b> Data formatting and Pre-processing</a>
@@ -513,7 +517,7 @@ <h1>
 <h1><span class="header-section-number">18</span> Contributing to Giotto<a href="contributing-to-giotto.html#contributing-to-giotto" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 <p>Jiaji George Chen</p>
 <p>August 7th 2024</p>
-<div class="sourceCode" id="cb330"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb330-1"><a href="contributing-to-giotto.html#cb330-1" tabindex="-1"></a>save_dir <span class="ot">&lt;-</span> <span class="st">&quot;~/Documents/GitHub/giotto_workshop_2024/img/03_session7&quot;</span></span></code></pre></div>
+<div class="sourceCode" id="cb337"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb337-1"><a href="contributing-to-giotto.html#cb337-1" tabindex="-1"></a>save_dir <span class="ot">&lt;-</span> <span class="st">&quot;~/Documents/GitHub/giotto_workshop_2024/img/03_session7&quot;</span></span></code></pre></div>
 <div id="contribution-guideline" class="section level2 hasAnchor" number="18.1">
 <h2><span class="header-section-number">18.1</span> Contribution guideline<a href="contributing-to-giotto.html#contribution-guideline" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p><a href="https://drieslab.github.io/Giotto_website/CONTRIBUTING.html" class="uri">https://drieslab.github.io/Giotto_website/CONTRIBUTING.html</a></p>

creating-a-giotto-object.html

@@ -186,7 +186,11 @@
 <ul>
 <li class="chapter" data-level="4.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#presentation-1"><i class="fa fa-check"></i><b>4.1</b> Presentation</a></li>
 <li class="chapter" data-level="4.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#ecosystem"><i class="fa fa-check"></i><b>4.2</b> Ecosystem</a></li>
-<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a></li>
+<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a>
+<ul>
+<li class="chapter" data-level="4.3.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-installation-1"><i class="fa fa-check"></i><b>4.3.1</b> Giotto installation</a></li>
+<li class="chapter" data-level="4.3.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#python-environment"><i class="fa fa-check"></i><b>4.3.2</b> Python environment</a></li>
+</ul></li>
 <li class="chapter" data-level="4.4" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-instructions"><i class="fa fa-check"></i><b>4.4</b> Giotto instructions</a></li>
 </ul></li>
 <li class="chapter" data-level="5" data-path="data-formatting-and-pre-processing.html"><a href="data-formatting-and-pre-processing.html"><i class="fa fa-check"></i><b>5</b> Data formatting and Pre-processing</a>
@@ -516,7 +520,7 @@ <h1><span class="header-section-number">6</span> Creating a Giotto object<a href
 <div id="used-packages" class="section level3 hasAnchor" number="6.0.1">
 <h3><span class="header-section-number">6.0.1</span> Used packages<a href="creating-a-giotto-object.html#used-packages" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <pre><code>Giotto      GiottoClass     GiottoData      pak</code></pre>
-<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb14-1"><a href="creating-a-giotto-object.html#cb14-1" tabindex="-1"></a>save_dir <span class="ot">&lt;-</span> <span class="st">&quot;~/Documents/GitHub/giotto_workshop_2024/img/01_session4&quot;</span></span></code></pre></div>
+<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb21-1"><a href="creating-a-giotto-object.html#cb21-1" tabindex="-1"></a>save_dir <span class="ot">&lt;-</span> <span class="st">&quot;~/Documents/GitHub/giotto_workshop_2024/img/01_session4&quot;</span></span></code></pre></div>
 </div>
 <div id="overview" class="section level2 hasAnchor" number="6.1">
 <h2><span class="header-section-number">6.1</span> Overview<a href="creating-a-giotto-object.html#overview" class="anchor-section" aria-label="Anchor link to header"></a></h2>
@@ -558,12 +562,12 @@ <h2><span class="header-section-number">6.6</span> Spatial plots<a href="creatin
 <p>Giotto has several spatial plotting functions.
 At the lowest level, you directly call <code>plot()</code> on several subobjects in order
 to see what they look like, particularly the ones containing spatial info.</p>
-<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb19-1"><a href="creating-a-giotto-object.html#cb19-1" tabindex="-1"></a>gpoints <span class="ot">&lt;-</span> GiottoData<span class="sc">::</span><span class="fu">loadSubObjectMini</span>(<span class="st">&quot;giottoPoints&quot;</span>)</span>
-<span id="cb19-2"><a href="creating-a-giotto-object.html#cb19-2" tabindex="-1"></a>gpoly <span class="ot">&lt;-</span> GiottoData<span class="sc">::</span><span class="fu">loadSubObjectMini</span>(<span class="st">&quot;giottoPolygon&quot;</span>)</span>
-<span id="cb19-3"><a href="creating-a-giotto-object.html#cb19-3" tabindex="-1"></a>spatlocs <span class="ot">&lt;-</span> GiottoData<span class="sc">::</span><span class="fu">loadSubObjectMini</span>(<span class="st">&quot;spatLocsObj&quot;</span>)</span>
-<span id="cb19-4"><a href="creating-a-giotto-object.html#cb19-4" tabindex="-1"></a>spatnet <span class="ot">&lt;-</span> GiottoData<span class="sc">::</span><span class="fu">loadSubObjectMini</span>(<span class="st">&quot;spatialNetworkObj&quot;</span>)</span>
-<span id="cb19-5"><a href="creating-a-giotto-object.html#cb19-5" tabindex="-1"></a>pca <span class="ot">&lt;-</span> GiottoData<span class="sc">::</span><span class="fu">loadSubObjectMini</span>(<span class="st">&quot;dimObj&quot;</span>)</span>
-<span id="cb19-6"><a href="creating-a-giotto-object.html#cb19-6" tabindex="-1"></a><span class="fu">plot</span>(pca, <span class="at">dims =</span> <span class="fu">c</span>(<span class="dv">3</span>,<span class="dv">10</span>))</span></code></pre></div>
+<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb26-1"><a href="creating-a-giotto-object.html#cb26-1" tabindex="-1"></a>gpoints <span class="ot">&lt;-</span> GiottoData<span class="sc">::</span><span class="fu">loadSubObjectMini</span>(<span class="st">&quot;giottoPoints&quot;</span>)</span>
+<span id="cb26-2"><a href="creating-a-giotto-object.html#cb26-2" tabindex="-1"></a>gpoly <span class="ot">&lt;-</span> GiottoData<span class="sc">::</span><span class="fu">loadSubObjectMini</span>(<span class="st">&quot;giottoPolygon&quot;</span>)</span>
+<span id="cb26-3"><a href="creating-a-giotto-object.html#cb26-3" tabindex="-1"></a>spatlocs <span class="ot">&lt;-</span> GiottoData<span class="sc">::</span><span class="fu">loadSubObjectMini</span>(<span class="st">&quot;spatLocsObj&quot;</span>)</span>
+<span id="cb26-4"><a href="creating-a-giotto-object.html#cb26-4" tabindex="-1"></a>spatnet <span class="ot">&lt;-</span> GiottoData<span class="sc">::</span><span class="fu">loadSubObjectMini</span>(<span class="st">&quot;spatialNetworkObj&quot;</span>)</span>
+<span id="cb26-5"><a href="creating-a-giotto-object.html#cb26-5" tabindex="-1"></a>pca <span class="ot">&lt;-</span> GiottoData<span class="sc">::</span><span class="fu">loadSubObjectMini</span>(<span class="st">&quot;dimObj&quot;</span>)</span>
+<span id="cb26-6"><a href="creating-a-giotto-object.html#cb26-6" tabindex="-1"></a><span class="fu">plot</span>(pca, <span class="at">dims =</span> <span class="fu">c</span>(<span class="dv">3</span>,<span class="dv">10</span>))</span></code></pre></div>
 </div>
 <div id="subsetting" class="section level2 hasAnchor" number="6.7">
 <h2><span class="header-section-number">6.7</span> Subsetting<a href="creating-a-giotto-object.html#subsetting" class="anchor-section" aria-label="Anchor link to header"></a></h2>
@@ -578,7 +582,7 @@ <h2><span class="header-section-number">6.8</span> Mini objects &amp; GiottoData
 <p>Giotto makes available several mini objects to allow devs and users to work
 with easily loadable Giotto objects. These are small subsets of a larger
 dataset that often contain some worked through analyses and are fully functional.</p>
-<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb20-1"><a href="creating-a-giotto-object.html#cb20-1" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pak</span>(<span class="st">&quot;drieslab/GiottoData&quot;</span>)</span></code></pre></div>
+<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb27-1"><a href="creating-a-giotto-object.html#cb27-1" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pak</span>(<span class="st">&quot;drieslab/GiottoData&quot;</span>)</span></code></pre></div>
 
 </div>
 </div>

data-formatting-and-pre-processing.html

@@ -186,7 +186,11 @@
 <ul>
 <li class="chapter" data-level="4.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#presentation-1"><i class="fa fa-check"></i><b>4.1</b> Presentation</a></li>
 <li class="chapter" data-level="4.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#ecosystem"><i class="fa fa-check"></i><b>4.2</b> Ecosystem</a></li>
-<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a></li>
+<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a>
+<ul>
+<li class="chapter" data-level="4.3.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-installation-1"><i class="fa fa-check"></i><b>4.3.1</b> Giotto installation</a></li>
+<li class="chapter" data-level="4.3.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#python-environment"><i class="fa fa-check"></i><b>4.3.2</b> Python environment</a></li>
+</ul></li>
 <li class="chapter" data-level="4.4" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-instructions"><i class="fa fa-check"></i><b>4.4</b> Giotto instructions</a></li>
 </ul></li>
 <li class="chapter" data-level="5" data-path="data-formatting-and-pre-processing.html"><a href="data-formatting-and-pre-processing.html"><i class="fa fa-check"></i><b>5</b> Data formatting and Pre-processing</a>
@@ -513,7 +517,7 @@ <h1>
 <h1><span class="header-section-number">5</span> Data formatting and Pre-processing<a href="data-formatting-and-pre-processing.html#data-formatting-and-pre-processing" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 <p>Jiaji George Chen</p>
 <p>August 5th 2024</p>
-<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="data-formatting-and-pre-processing.html#cb12-1" tabindex="-1"></a>save_dir <span class="ot">&lt;-</span> <span class="st">&quot;~/Documents/GitHub/giotto_workshop_2024/img/01_session3&quot;</span></span></code></pre></div>
+<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb19-1"><a href="data-formatting-and-pre-processing.html#cb19-1" tabindex="-1"></a>save_dir <span class="ot">&lt;-</span> <span class="st">&quot;~/Documents/GitHub/giotto_workshop_2024/img/01_session3&quot;</span></span></code></pre></div>
 <div id="data-formats" class="section level2 hasAnchor" number="5.1">
 <h2><span class="header-section-number">5.1</span> Data formats<a href="data-formatting-and-pre-processing.html#data-formats" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>.h5</p>

datasets-packages.html

@@ -186,7 +186,11 @@
 <ul>
 <li class="chapter" data-level="4.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#presentation-1"><i class="fa fa-check"></i><b>4.1</b> Presentation</a></li>
 <li class="chapter" data-level="4.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#ecosystem"><i class="fa fa-check"></i><b>4.2</b> Ecosystem</a></li>
-<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a></li>
+<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a>
+<ul>
+<li class="chapter" data-level="4.3.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-installation-1"><i class="fa fa-check"></i><b>4.3.1</b> Giotto installation</a></li>
+<li class="chapter" data-level="4.3.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#python-environment"><i class="fa fa-check"></i><b>4.3.2</b> Python environment</a></li>
+</ul></li>
 <li class="chapter" data-level="4.4" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-instructions"><i class="fa fa-check"></i><b>4.4</b> Giotto instructions</a></li>
 </ul></li>
 <li class="chapter" data-level="5" data-path="data-formatting-and-pre-processing.html"><a href="data-formatting-and-pre-processing.html"><i class="fa fa-check"></i><b>5</b> Data formatting and Pre-processing</a>

index.html

@@ -186,7 +186,11 @@
 <ul>
 <li class="chapter" data-level="4.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#presentation-1"><i class="fa fa-check"></i><b>4.1</b> Presentation</a></li>
 <li class="chapter" data-level="4.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#ecosystem"><i class="fa fa-check"></i><b>4.2</b> Ecosystem</a></li>
-<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a></li>
+<li class="chapter" data-level="4.3" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#installation-python-environment"><i class="fa fa-check"></i><b>4.3</b> Installation + python environment</a>
+<ul>
+<li class="chapter" data-level="4.3.1" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-installation-1"><i class="fa fa-check"></i><b>4.3.1</b> Giotto installation</a></li>
+<li class="chapter" data-level="4.3.2" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#python-environment"><i class="fa fa-check"></i><b>4.3.2</b> Python environment</a></li>
+</ul></li>
 <li class="chapter" data-level="4.4" data-path="introduction-to-the-giotto-package.html"><a href="introduction-to-the-giotto-package.html#giotto-instructions"><i class="fa fa-check"></i><b>4.4</b> Giotto instructions</a></li>
 </ul></li>
 <li class="chapter" data-level="5" data-path="data-formatting-and-pre-processing.html"><a href="data-formatting-and-pre-processing.html"><i class="fa fa-check"></i><b>5</b> Data formatting and Pre-processing</a>