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<!DOCTYPE html>
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<title>Chapter 3 Beta diversity mapping description | MicrobioSee User Manual</title>
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<meta name="author" content="Jinhui Li, Yimeng Sang, Sen Zeng." />
<meta name="date" content="2021-12-01" />
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<li><a href="https://microbiosee.gxu.edu.cn">MicrobioSee Guide</a></li>
<li class="divider"></li>
<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> MicrobioSee Users’ Guide</a>
<ul>
<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#microbiosee-a-visualization-tool-for-microbial-multiomics."><i class="fa fa-check"></i><b>1.1</b> Microbiosee: a visualization tool for microbial multiomics.</a></li>
<li class="chapter" data-level="1.2" data-path="index.html"><a href="index.html#issues-and-contact"><i class="fa fa-check"></i><b>1.2</b> Issues and Contact</a></li>
<li class="chapter" data-level="1.3" data-path="index.html"><a href="index.html#license"><i class="fa fa-check"></i><b>1.3</b> License</a></li>
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<li class="chapter" data-level="2" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html"><i class="fa fa-check"></i><b>2</b> Alpha diversity mapping description</a>
<ul>
<li class="chapter" data-level="2.1" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#upload-sample-data"><i class="fa fa-check"></i><b>2.1</b> Upload sample data</a></li>
<li class="chapter" data-level="2.2" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#different-alpha-index-values-and-statistical-methods"><i class="fa fa-check"></i><b>2.2</b> Different alpha index values ,and statistical methods</a></li>
<li class="chapter" data-level="2.3" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#different-drawing-tools"><i class="fa fa-check"></i><b>2.3</b> Different drawing tools</a>
<ul>
<li class="chapter" data-level="2.3.1" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#box-plot"><i class="fa fa-check"></i><b>2.3.1</b> box-plot</a></li>
<li class="chapter" data-level="2.3.2" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#pirates"><i class="fa fa-check"></i><b>2.3.2</b> pirates</a></li>
<li class="chapter" data-level="2.3.3" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#cloudyrain"><i class="fa fa-check"></i><b>2.3.3</b> cloudyrain</a></li>
<li class="chapter" data-level="2.3.4" data-path="alpha-diversity-mapping-description.html"><a href="alpha-diversity-mapping-description.html#violin"><i class="fa fa-check"></i><b>2.3.4</b> violin</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="3" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html"><i class="fa fa-check"></i><b>3</b> Beta diversity mapping description</a>
<ul>
<li class="chapter" data-level="3.1" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#upload-sample-data-1"><i class="fa fa-check"></i><b>3.1</b> Upload sample data</a></li>
<li class="chapter" data-level="3.2" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#different-beta-diversity-analysis-tools"><i class="fa fa-check"></i><b>3.2</b> Different beta diversity analysis tools</a>
<ul>
<li class="chapter" data-level="3.2.1" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#different-drawing-tools-1"><i class="fa fa-check"></i><b>3.2.1</b> Different drawing tools</a></li>
<li class="chapter" data-level="3.2.2" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#pcoa"><i class="fa fa-check"></i><b>3.2.2</b> PCoA</a></li>
<li class="chapter" data-level="3.2.3" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#pca"><i class="fa fa-check"></i><b>3.2.3</b> PCA</a></li>
<li class="chapter" data-level="3.2.4" data-path="beta-diversity-mapping-description.html"><a href="beta-diversity-mapping-description.html#nmds"><i class="fa fa-check"></i><b>3.2.4</b> NMDS</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="stack-column-charts-mapping-description.html"><a href="stack-column-charts-mapping-description.html"><i class="fa fa-check"></i><b>4</b> Stack column charts mapping description</a>
<ul>
<li class="chapter" data-level="4.1" data-path="stack-column-charts-mapping-description.html"><a href="stack-column-charts-mapping-description.html#upload-sample-data-2"><i class="fa fa-check"></i><b>4.1</b> Upload sample data</a></li>
<li class="chapter" data-level="4.2" data-path="stack-column-charts-mapping-description.html"><a href="stack-column-charts-mapping-description.html#draw"><i class="fa fa-check"></i><b>4.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="venn-mapping-description.html"><a href="venn-mapping-description.html"><i class="fa fa-check"></i><b>5</b> Venn mapping description</a>
<ul>
<li class="chapter" data-level="5.1" data-path="venn-mapping-description.html"><a href="venn-mapping-description.html#upload-sample-data-3"><i class="fa fa-check"></i><b>5.1</b> Upload sample data</a></li>
<li class="chapter" data-level="5.2" data-path="venn-mapping-description.html"><a href="venn-mapping-description.html#draw-1"><i class="fa fa-check"></i><b>5.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="6" data-path="upset-mapping-description.html"><a href="upset-mapping-description.html"><i class="fa fa-check"></i><b>6</b> Upset mapping description</a>
<ul>
<li class="chapter" data-level="6.1" data-path="upset-mapping-description.html"><a href="upset-mapping-description.html#upload-sample-data-4"><i class="fa fa-check"></i><b>6.1</b> Upload sample data</a></li>
<li class="chapter" data-level="6.2" data-path="upset-mapping-description.html"><a href="upset-mapping-description.html#draw-2"><i class="fa fa-check"></i><b>6.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="bubble-mapping-description.html"><a href="bubble-mapping-description.html"><i class="fa fa-check"></i><b>7</b> Bubble mapping description</a>
<ul>
<li class="chapter" data-level="7.1" data-path="bubble-mapping-description.html"><a href="bubble-mapping-description.html#upload-sample-data-5"><i class="fa fa-check"></i><b>7.1</b> Upload sample data</a></li>
<li class="chapter" data-level="7.2" data-path="bubble-mapping-description.html"><a href="bubble-mapping-description.html#draw-3"><i class="fa fa-check"></i><b>7.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="volcano-mapping-description.html"><a href="volcano-mapping-description.html"><i class="fa fa-check"></i><b>8</b> Volcano mapping description</a>
<ul>
<li class="chapter" data-level="8.1" data-path="volcano-mapping-description.html"><a href="volcano-mapping-description.html#upload-sample-data-6"><i class="fa fa-check"></i><b>8.1</b> Upload sample data</a></li>
<li class="chapter" data-level="8.2" data-path="volcano-mapping-description.html"><a href="volcano-mapping-description.html#draw-4"><i class="fa fa-check"></i><b>8.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="scatter-mapping-description.html"><a href="scatter-mapping-description.html"><i class="fa fa-check"></i><b>9</b> Scatter mapping description</a>
<ul>
<li class="chapter" data-level="9.1" data-path="scatter-mapping-description.html"><a href="scatter-mapping-description.html#upload-sample-data-7"><i class="fa fa-check"></i><b>9.1</b> Upload sample data</a></li>
<li class="chapter" data-level="9.2" data-path="scatter-mapping-description.html"><a href="scatter-mapping-description.html#draw-5"><i class="fa fa-check"></i><b>9.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="10" data-path="rose-mapping-description.html"><a href="rose-mapping-description.html"><i class="fa fa-check"></i><b>10</b> Rose mapping description</a>
<ul>
<li class="chapter" data-level="10.1" data-path="rose-mapping-description.html"><a href="rose-mapping-description.html#upload-sample-data-8"><i class="fa fa-check"></i><b>10.1</b> Upload sample data</a></li>
<li class="chapter" data-level="10.2" data-path="rose-mapping-description.html"><a href="rose-mapping-description.html#draw-6"><i class="fa fa-check"></i><b>10.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html"><i class="fa fa-check"></i><b>11</b> 3Dmol mapping description</a>
<ul>
<li class="chapter" data-level="11.1" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html#upload-sample-data-9"><i class="fa fa-check"></i><b>11.1</b> Upload sample data</a></li>
<li class="chapter" data-level="11.2" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html#draw-7"><i class="fa fa-check"></i><b>11.2</b> Draw</a></li>
<li class="chapter" data-level="11.3" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html#the-tool-provides-two-ways-to-draw-3d-drawings."><i class="fa fa-check"></i><b>11.3</b> The tool provides two ways to draw 3d drawings.</a>
<ul>
<li class="chapter" data-level="11.3.1" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html#datafile-way"><i class="fa fa-check"></i><b>11.3.1</b> Datafile way</a></li>
<li class="chapter" data-level="11.3.2" data-path="dmol-mapping-description.html"><a href="dmol-mapping-description.html#pdb-id-way"><i class="fa fa-check"></i><b>11.3.2</b> PDB id way</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="12" data-path="rose-mapping-description-1.html"><a href="rose-mapping-description-1.html"><i class="fa fa-check"></i><b>12</b> Rose mapping description</a>
<ul>
<li class="chapter" data-level="12.1" data-path="rose-mapping-description-1.html"><a href="rose-mapping-description-1.html#upload-sample-data-10"><i class="fa fa-check"></i><b>12.1</b> Upload sample data</a></li>
<li class="chapter" data-level="12.2" data-path="rose-mapping-description-1.html"><a href="rose-mapping-description-1.html#draw-8"><i class="fa fa-check"></i><b>12.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="histogram-mapping-description.html"><a href="histogram-mapping-description.html"><i class="fa fa-check"></i><b>13</b> Histogram mapping description</a>
<ul>
<li class="chapter" data-level="13.1" data-path="histogram-mapping-description.html"><a href="histogram-mapping-description.html#upload-sample-data-11"><i class="fa fa-check"></i><b>13.1</b> Upload sample data</a></li>
<li class="chapter" data-level="13.2" data-path="histogram-mapping-description.html"><a href="histogram-mapping-description.html#draw-9"><i class="fa fa-check"></i><b>13.2</b> draw</a></li>
</ul></li>
<li class="chapter" data-level="14" data-path="pie-mapping-description.html"><a href="pie-mapping-description.html"><i class="fa fa-check"></i><b>14</b> Pie mapping description</a>
<ul>
<li class="chapter" data-level="14.1" data-path="pie-mapping-description.html"><a href="pie-mapping-description.html#upload-sample-data-12"><i class="fa fa-check"></i><b>14.1</b> Upload sample data</a></li>
<li class="chapter" data-level="14.2" data-path="pie-mapping-description.html"><a href="pie-mapping-description.html#draw-10"><i class="fa fa-check"></i><b>14.2</b> draw</a></li>
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<div id="beta-diversity-mapping-description" class="section level1" number="3">
<h1><span class="header-section-number">Chapter 3</span> Beta diversity mapping description</h1>
<div id="upload-sample-data-1" class="section level2" number="3.1">
<h2><span class="header-section-number">3.1</span> Upload sample data</h2>
<p>You need to upload two data files including <strong>sample OTU result file</strong> and <strong>metadata file</strong>.</p>
<p>Such as</p>
<table>
<colgroup>
<col width="2%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="2%" />
<col width="2%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
<col width="3%" />
</colgroup>
<thead>
<tr class="header">
<th>Sample</th>
<th>Achimill</th>
<th>Agrostol</th>
<th>Airaprae</th>
<th>Alopgeni</th>
<th>Anthodor</th>
<th>Bellpere</th>
<th>Bromhord</th>
<th>Chenalbu</th>
<th>Cirsarve</th>
<th>Comapalu</th>
<th>Eleopalu</th>
<th>Elymrepe</th>
<th>Empenigr</th>
<th>Hyporadi</th>
<th>Juncarti</th>
<th>Juncbufo</th>
<th>Lolipere</th>
<th>Planlanc</th>
<th>Poaprat</th>
<th>Poatriv</th>
<th>Ranuflam</th>
<th>Rumeacet</th>
<th>Sagiproc</th>
<th>Salirepe</th>
<th>Scorautu</th>
<th>Trifprat</th>
<th>Trifrepe</th>
<th>Vicilath</th>
<th>Bracruta</th>
<th>Callcusp</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>1</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>4</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>7</td>
<td>0</td>
<td>4</td>
<td>2</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr class="even">
<td>2</td>
<td>3</td>
<td>0</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>3</td>
<td>4</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>4</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>5</td>
<td>0</td>
<td>4</td>
<td>7</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>5</td>
<td>0</td>
<td>5</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr class="odd">
<td>3</td>
<td>0</td>
<td>4</td>
<td>0</td>
<td>7</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>4</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>6</td>
<td>0</td>
<td>5</td>
<td>6</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>2</td>
<td>0</td>
</tr>
<tr class="even">
<td>4</td>
<td>0</td>
<td>8</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>2</td>
<td>3</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>0</td>
<td>4</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>5</td>
<td>0</td>
<td>4</td>
<td>5</td>
<td>0</td>
<td>0</td>
<td>5</td>
<td>0</td>
<td>2</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>2</td>
<td>0</td>
</tr>
<tr class="odd">
<td>5</td>
<td>2</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>4</td>
<td>2</td>
<td>2</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>4</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>2</td>
<td>5</td>
<td>2</td>
<td>6</td>
<td>0</td>
<td>5</td>
<td>0</td>
<td>0</td>
<td>3</td>
<td>2</td>
<td>2</td>
<td>0</td>
<td>2</td>
<td>0</td>
</tr>
</tbody>
</table>
<p>The first column is the sample id,the other column is the abundance of each indicator in different samples.</p>
<table>
<thead>
<tr class="header">
<th>Sample</th>
<th>group</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>1</td>
<td>SF</td>
</tr>
<tr class="even">
<td>2</td>
<td>BF</td>
</tr>
<tr class="odd">
<td>3</td>
<td>SF</td>
</tr>
<tr class="even">
<td>4</td>
<td>SF</td>
</tr>
<tr class="odd">
<td>5</td>
<td>HF</td>
</tr>
<tr class="even">
<td>6</td>
<td>HF</td>
</tr>
<tr class="odd">
<td>7</td>
<td>HF</td>
</tr>
<tr class="even">
<td>8</td>
<td>HF</td>
</tr>
<tr class="odd">
<td>9</td>
<td>HF</td>
</tr>
</tbody>
</table>
<p>The first column is the sample id,the second column is the grouping of samples.</p>
<p><strong>Paying attention, please ,you need to upload the file in the format of the sample data</strong>.</p>
</div>
<div id="different-beta-diversity-analysis-tools" class="section level2" number="3.2">
<h2><span class="header-section-number">3.2</span> Different beta diversity analysis tools</h2>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153833.png" style="zoom: 50%;" /></p>
<div id="different-drawing-tools-1" class="section level3" number="3.2.1">
<h3><span class="header-section-number">3.2.1</span> Different drawing tools</h3>
</div>
<div id="pcoa" class="section level3" number="3.2.2">
<h3><span class="header-section-number">3.2.2</span> PCoA</h3>
<p><strong>Dissimilarity index</strong>, partial match to “manhattan,” “euclidean,” “canberra,” “clark,” “bray,” “kulczynski,” “jaccard,” “gower,” “altGower,” “morisita,” “horn,” “mountford,” “raup,” “binomial,” “chao,” “cao,” “mahalanobis,” “chisq” or “chord.”</p>
<p><strong>The Jaccard and Bray-curtis dissimilarity</strong> coefficients are <strong>commonly</strong> used in bioinformatics analysis and are the basis for calculating species similarity.</p>
<p>It should be noted that the focus of these two dissimilarity coefficients is different.</p>
<p>In analysis, Jaccard only considers the presence or absence of species in the sample, not the abundance.</p>
<p>The Bray-curtis calculation not only considers the presence or absence of species in the sample, but also considers the relative abundance of different species.</p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153834.png" style="zoom:33%;" /><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153835.png" style="zoom:33%;" /></p>
<p>This button can choose whether to perform <strong>R-value and P-value</strong> calculations on the data.
R^2 can quantify the strength of the relationship between the model response variable and the dependent variable.
The p-value test can determine how reliable the fitted equation is.</p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153836.png" style="zoom:33%;" /><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153837.png" style="zoom:33%;" /></p>
</div>
<div id="pca" class="section level3" number="3.2.3">
<h3><span class="header-section-number">3.2.3</span> PCA</h3>
<p>Whether to add labels to each point</p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153838.png" style="zoom:33%;" /><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153839.png" style="zoom:33%;" /></p>
<p>Adjust label position</p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153840.png" style="zoom:33%;" /><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153841.png" style="zoom:33%;" /></p>
<p>Adjust label font size</p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153842.png" style="zoom:33%;" /><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153843.png" style="zoom:33%;" /></p>
<p>Adjust the aspect ratio of the drawing</p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153844.png" style="zoom:33%;" /><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153845.png" style="zoom:33%;" /></p>
</div>
<div id="nmds" class="section level3" number="3.2.4">
<h3><span class="header-section-number">3.2.4</span> NMDS</h3>
<p>The function offers different standardization methods for community data:</p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153846.png" /></p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153847.png" style="zoom:33%;" /></p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153848.png" style="zoom:33%;" /></p>
<p><strong>Dissimilarity index,</strong> partial match to “manhattan,” “euclidean,” “canberra,” “clark,” “bray,” “kulczynski,” “jaccard,” “gower,” “altGower,” “morisita,” “horn,” “mountford,” “raup,” “binomial,” “chao,” “cao,” “mahalanobis,” “chisq” or “chord.”<strong>It is the same as PCA distance matrix method.</strong></p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153849.png" style="zoom:33%;" /></p>
<p><img src="https://gitee.com/li-jinhui/tuchuang/raw/master/img99/202201112153850.png" style="zoom:33%;" /></p>
</div>
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</div>
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