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@TuomasBorman
TuomasBorman committed Sep 3, 2024
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2 changes: 1 addition & 1 deletion docs/devel/index.html
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Expand Up @@ -554,7 +554,7 @@ <h1 class="title">Orchestrating Microbiome Analysis</h1>
<div class="quarto-layout-panel" data-layout-ncol="2">
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<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<p><strong>Package:</strong> OMA<br><strong>Authors:<br></strong> - Leo Lahti [aut]<br> - Tuomas Borman [aut, cre]<br> - Felix GM Ernst [aut]<br> - and others (see the full list of contributors) [ctb]<br><strong>Compiled:</strong> 2024-09-02<br><strong>Package version:</strong> 0.98.25<br><strong>R version:</strong> R version 4.4.1 (2024-06-14)<br><strong>BioC version:</strong> 3.20<br><strong>License:</strong> CC BY-NC-SA 4.0<br></p>
<p><strong>Package:</strong> OMA<br><strong>Authors:<br></strong> - Leo Lahti [aut]<br> - Tuomas Borman [aut, cre]<br> - Felix GM Ernst [aut]<br> - and others (see the full list of contributors) [ctb]<br><strong>Compiled:</strong> 2024-09-03<br><strong>Package version:</strong> 0.98.25<br><strong>R version:</strong> R version 4.4.1 (2024-06-14)<br><strong>BioC version:</strong> 3.20<br><strong>License:</strong> CC BY-NC-SA 4.0<br></p>
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<div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
<p><img src="assets/cover.png" align="middle" style="max-width:100%;
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12 changes: 6 additions & 6 deletions docs/devel/pages/beta_diversity.html
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Expand Up @@ -1130,7 +1130,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
<td style="text-align: right;">6</td>
<td style="text-align: right;">1.1157</td>
<td style="text-align: right;">1.940</td>
<td style="text-align: right;">0.045</td>
<td style="text-align: right;">0.028</td>
<td style="text-align: right;">3.991</td>
<td style="text-align: right;">0.2795</td>
</tr>
Expand All @@ -1139,7 +1139,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
<td style="text-align: right;">4</td>
<td style="text-align: right;">0.5837</td>
<td style="text-align: right;">1.522</td>
<td style="text-align: right;">0.154</td>
<td style="text-align: right;">0.155</td>
<td style="text-align: right;">3.991</td>
<td style="text-align: right;">0.1463</td>
</tr>
Expand All @@ -1148,7 +1148,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
<td style="text-align: right;">1</td>
<td style="text-align: right;">0.1679</td>
<td style="text-align: right;">1.751</td>
<td style="text-align: right;">0.102</td>
<td style="text-align: right;">0.093</td>
<td style="text-align: right;">3.991</td>
<td style="text-align: right;">0.0421</td>
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<td style="text-align: right;">0.0628</td>
<td style="text-align: right;">2.7440</td>
<td style="text-align: right;">999</td>
<td style="text-align: right;">0.121</td>
<td style="text-align: right;">0.118</td>
<td style="text-align: right;">1.0288</td>
<td style="text-align: right;">0.2440</td>
</tr>
Expand All @@ -1288,7 +1288,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
<td style="text-align: right;">0.0103</td>
<td style="text-align: right;">0.4158</td>
<td style="text-align: right;">999</td>
<td style="text-align: right;">0.537</td>
<td style="text-align: right;">0.531</td>
<td style="text-align: right;">0.9283</td>
<td style="text-align: right;">0.0111</td>
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Expand All @@ -1299,7 +1299,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
<td style="text-align: right;">0.0113</td>
<td style="text-align: right;">17.0255</td>
<td style="text-align: right;">999</td>
<td style="text-align: right;">0.412</td>
<td style="text-align: right;">0.401</td>
<td style="text-align: right;">0.3319</td>
<td style="text-align: right;">0.9860</td>
</tr>
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34 changes: 14 additions & 20 deletions docs/devel/pages/extra_material.html
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Expand Up @@ -1293,7 +1293,7 @@ <h1 class="title"><span id="sec-extras" class="quarto-section-identifier">Append
<p>Printing a summary about the posterior:</p>
<div class="cell" data-layout-align="center">
<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu"><a href="https://jsilve24.github.io/fido/reference/ppc_summary.html">ppc_summary</a></span><span class="op">(</span><span class="va">posterior</span><span class="op">)</span></span>
<span><span class="co">## Proportions of Observations within 95% Credible Interval: 0.9968944</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span><span class="co">## Proportions of Observations within 95% Credible Interval: 0.9967794</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p>Plotting the summary of the posterior distributions of the regression parameters:</p>
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Expand Down Expand Up @@ -1484,12 +1484,12 @@ <h1 class="title"><span id="sec-extras" class="quarto-section-identifier">Append
<span><span class="co">## call:</span></span>
<span><span class="co">## biclust(x = corr, method = BCPlaid(), verbose = FALSE)</span></span>
<span><span class="co">## </span></span>
<span><span class="co">## Number of Clusters found: 4 </span></span>
<span><span class="co">## Number of Clusters found: 3 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## First 4 Cluster sizes:</span></span>
<span><span class="co">## BC 1 BC 2 BC 3 BC 4</span></span>
<span><span class="co">## Number of Rows: 15 17 19 2</span></span>
<span><span class="co">## Number of Columns: 13 14 9 11</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span><span class="co">## First 3 Cluster sizes:</span></span>
<span><span class="co">## BC 1 BC 2 BC 3</span></span>
<span><span class="co">## Number of Rows: 16 15 16</span></span>
<span><span class="co">## Number of Columns: 13 14 10</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p>The object includes cluster information. However compared to <code>cobiclust</code>, <code>biclust</code> object includes only information about clusters that were found, not general cluster.</p>
<p>Meaning that if one cluster size of 5 features was found out of 20 features, those 15 features do not belong to any cluster. That is why we have to create an additional cluster for features/samples that are not assigned into any cluster.</p>
Expand Down Expand Up @@ -1554,13 +1554,13 @@ <h1 class="title"><span id="sec-extras" class="quarto-section-identifier">Append
<span></span>
<span><span class="co"># Print biclusters for rows</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">bicluster_rows</span><span class="op">)</span></span>
<span><span class="co">## cluster_1 cluster_2 cluster_3 cluster_4 cluster_5</span></span>
<span><span class="co">## Ambiguous_taxa_1 FALSE FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_3 TRUE FALSE TRUE FALSE FALSE</span></span>
<span><span class="co">## Ambiguous_taxa_4 FALSE FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_5 FALSE FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_7 FALSE FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_9 FALSE FALSE FALSE FALSE TRUE</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span><span class="co">## cluster_1 cluster_2 cluster_3 cluster_4</span></span>
<span><span class="co">## Ambiguous_taxa_1 FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_3 TRUE FALSE TRUE FALSE</span></span>
<span><span class="co">## Ambiguous_taxa_4 FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_5 FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_7 FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_9 FALSE FALSE FALSE TRUE</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p>Let’s collect information for the scatter plot.</p>
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Expand Down Expand Up @@ -1632,16 +1632,10 @@ <h1 class="title"><span id="sec-extras" class="quarto-section-identifier">Append
</figure>
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<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure class="figure"><p><img src="extra_material_files/figure-html/biclust_7-5.png" class="img-fluid quarto-figure quarto-figure-center figure-img" style="width:33.0%"></p>
</figure>
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<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">pics</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span> <span class="op">+</span> <span class="va">pics</span><span class="op">[[</span><span class="fl">2</span><span class="op">]</span><span class="op">]</span> <span class="op">+</span> <span class="va">pics</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure class="figure"><p><img src="extra_material_files/figure-html/biclust_7-6.png" class="img-fluid quarto-figure quarto-figure-center figure-img" style="width:33.0%"></p>
<figure class="figure"><p><img src="extra_material_files/figure-html/biclust_7-5.png" class="img-fluid quarto-figure quarto-figure-center figure-img" style="width:33.0%"></p>
</figure>
</div>
</div>
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2 changes: 1 addition & 1 deletion docs/devel/pages/introductory_workflow.html
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Expand Up @@ -809,7 +809,7 @@ <h1 class="title">
<span><span class="co">## colLinks: NULL</span></span>
<span><span class="co">## colTree: NULL</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Great! Now, our data is aggregated to the taxonomic information up to the Phylum level, allowing the analysis to be focused on this specific rank. Although we won’t use the agglomerated data in the rest of the workflow, all the code below can also be applied to it.</p>
<p>Great! Now, our data is aggregated to the taxonomic information up to the Phylum level, allowing the analysis to be focused on this specific rank.</p>
</section><section id="transformation" class="level3" data-number="26.5.2"><h3 data-number="26.5.2" class="anchored" data-anchor-id="transformation">
<span class="header-section-number">26.5.2</span> Transformation</h3>
<p>The <a href="https://microbiome.github.io/mia/"><code>mia</code> package</a> provides an easy way to calculate the relative abundances for our <code>TreeSE</code> using the <code>transformAssay()</code> method.</p>
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28 changes: 14 additions & 14 deletions docs/devel/pages/introductory_workflow_dutch_version.html
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22 changes: 11 additions & 11 deletions docs/devel/pages/introductory_workflow_french_version.html
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