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@antagomir
antagomir committed Jul 29, 2024
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12 changes: 6 additions & 6 deletions docs/devel/pages/beta_diversity.html
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Expand Up @@ -1129,7 +1129,7 @@ <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;">0.026</td>
<td style="text-align: right;">0.042</td>
<td style="text-align: right;">3.991</td>
<td style="text-align: right;">0.2795</td>
</tr>
Expand All @@ -1138,7 +1138,7 @@ <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;">0.151</td>
<td style="text-align: right;">0.139</td>
<td style="text-align: right;">3.991</td>
<td style="text-align: right;">0.1463</td>
</tr>
Expand All @@ -1147,7 +1147,7 @@ <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;">0.109</td>
<td style="text-align: right;">0.113</td>
<td style="text-align: right;">3.991</td>
<td style="text-align: right;">0.0421</td>
</tr>
Expand Down Expand Up @@ -1276,7 +1276,7 @@ <h1 class="title"><span id="sec-community-similarity" class="quarto-section-iden
<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;">0.099</td>
<td style="text-align: right;">0.117</td>
<td style="text-align: right;">1.0288</td>
<td style="text-align: right;">0.2440</td>
</tr>
Expand All @@ -1287,7 +1287,7 @@ <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;">0.536</td>
<td style="text-align: right;">0.520</td>
<td style="text-align: right;">0.9283</td>
<td style="text-align: right;">0.0111</td>
</tr>
Expand All @@ -1298,7 +1298,7 @@ <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;">0.428</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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39 changes: 29 additions & 10 deletions docs/devel/pages/extra_material.html
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Expand Up @@ -1290,7 +1290,7 @@ <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: 0.9982747</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Plotting the summary of the posterior distributions of the regression parameters:</p>
<div class="cell" data-layout-align="center">
Expand Down Expand Up @@ -1481,12 +1481,12 @@ <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: 5 </span></span>
<span><span class="co">## Number of Clusters found: 7 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## First 5 Cluster sizes:</span></span>
<span><span class="co">## BC 1 BC 2 BC 3 BC 4 BC 5</span></span>
<span><span class="co">## Number of Rows: 18 14 17 2 7</span></span>
<span><span class="co">## Number of Columns: 13 14 7 13 9</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span><span class="co">## Number of Rows: 17 14 16 4 5</span></span>
<span><span class="co">## Number of Columns: 13 14 9 12 8</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>The object includes cluster information. However compared to <em>cobiclust</em>, <em>biclust</em> 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 @@ -1552,12 +1552,19 @@ <h1 class="title"><span id="sec-extras" class="quarto-section-identifier">Append
<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 cluster_6</span></span>
<span><span class="co">## Ambiguous_taxa_1 FALSE FALSE FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_1 FALSE FALSE FALSE FALSE FALSE FALSE</span></span>
<span><span class="co">## Ambiguous_taxa_3 TRUE FALSE TRUE FALSE FALSE FALSE</span></span>
<span><span class="co">## Ambiguous_taxa_4 FALSE FALSE FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_5 FALSE FALSE FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_7 FALSE FALSE FALSE FALSE FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_9 FALSE 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">## Ambiguous_taxa_4 FALSE FALSE FALSE FALSE FALSE FALSE</span></span>
<span><span class="co">## Ambiguous_taxa_5 FALSE FALSE FALSE FALSE FALSE FALSE</span></span>
<span><span class="co">## Ambiguous_taxa_7 FALSE FALSE FALSE FALSE FALSE FALSE</span></span>
<span><span class="co">## Ambiguous_taxa_9 FALSE FALSE FALSE FALSE FALSE FALSE</span></span>
<span><span class="co">## cluster_7 cluster_8</span></span>
<span><span class="co">## Ambiguous_taxa_1 FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_3 FALSE FALSE</span></span>
<span><span class="co">## Ambiguous_taxa_4 FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_5 FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_7 FALSE TRUE</span></span>
<span><span class="co">## Ambiguous_taxa_9 FALSE TRUE</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Let’s collect information for the scatter plot.</p>
<div class="cell" data-layout-align="center">
Expand Down Expand Up @@ -1641,13 +1648,25 @@ <h1 class="title"><span id="sec-extras" class="quarto-section-identifier">Append
</figure>
</div>
</div>
<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_7-7.png" class="img-fluid quarto-figure quarto-figure-center figure-img" style="width:33.0%"></p>
</figure>
</div>
</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_7-8.png" class="img-fluid quarto-figure quarto-figure-center figure-img" style="width:33.0%"></p>
</figure>
</div>
</div>
<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_7-9.png" class="img-fluid quarto-figure quarto-figure-center figure-img" style="width:33.0%"></p>
</figure>
</div>
</div>
</div>
<p><em>pheatmap</em> does not allow boolean values, so they must be converted into factors.</p>
<div class="cell" data-layout-align="center">
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24 changes: 12 additions & 12 deletions docs/devel/pages/introductory_workflow.html
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26 changes: 13 additions & 13 deletions docs/devel/pages/introductory_workflow_dutch_version.html
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24 changes: 12 additions & 12 deletions docs/devel/pages/introductory_workflow_french_version.html
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