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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>MicrobioSee User Manual</title>
<meta name="MicrobioSee" content="MicrobioSee User Manual" />
<meta name="KEYWORDS" content="MicrobioSee,plot,visualization" />
<meta property="og:title" content="MicrobioSee User Manual" />
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<meta name="twitter:title" content="MicrobioSee User Manual" />
<meta name="referrer" content="no-referrer" />
<meta name="author" content="Jinhui Li, Yimeng Sang, Sen Zeng." />
<meta name="date" content="2021-12-01" />
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<meta name="apple-mobile-web-app-capable" content="yes" />
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<div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
<div class="book-summary">
<nav role="navigation">
<ul class="summary">
<li><a href="https://microbiosee.gxu.edu.cn">MicrobioSee</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>
</ul></li>
<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>
</ul></li>
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<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
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<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">MicrobioSee User Manual</a>
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<h1 class="title" color="red">MicrobioSee</h1>
<p class="author"><em>Jinhui Li, Yimeng Sang, Sen Zeng.</em></p>
<p class="date"><em>2021-01-01</em></p>
</div>
<img src="https://microbiosee.gxu.edu.cn/images/pic01.jpg">
<div id="microbiosee-users-guide" class="section level1" number="1">
<h1><span class="header-section-number">Chapter 1</span> User Guide for MicrobioSee</h1>
<div id="microbiosee-a-visualization-tool-for-microbial-multiomics." class="section level2" number="1.1">
<h2><span class="header-section-number">1.1</span> Microbiosee: a visualization tool for microbial multiomics.</h2>
<blockquote>
<p>Welcome!
Click:<a href="http://microbiosee.gxu.edu.cn/" class="uri">http://microbiosee.gxu.edu.cn/</a></p>
</blockquote>
<ul>
<li>This book guides the readers to be familiar with MicrobioSee, a toolkit for data visualization. It also introduces basic plotting, which aims to make the process of microbiome data visualization. This book was created entirely using Gitbook Editor for reproducibility.
Note: If you are interested in recreating this figure, please read this book.
</li>
<li>Please cite this paper when MicrobioSee is used. <br></li>
<blockquote>
Jinhui Li, Yimeng Sang, Sen Zeng, Shuming Mo, Zufan Zhang, Sheng He, Xinying Li, Jianping Liao*, and Chengjian Jiang*. MicrobioSee: a web-based visualization toolkit for multi-omics of microbiology. 2022. DOI: <a href="https://doi.org/10.3389/fgene.2022.853612"> 10.3389/fgene.2022.853612</a>.
</blockquote>
</ul>
</div>
<div id="issues-and-contact" class="section level2" number="1.2">
<h2><span class="header-section-number">1.2</span> Issues and Contact</h2>
<ul>
<li>If you spot any mistakes in this online book, please pull-request on <a href="https://github.com/MicrobioSee/MicrobioSee">Github</a> or email <a href="mailto:[email protected]" class="email">[email protected]</a>. If you find issues with the ‘MicrobioSee’ project, please pull-request on Github .</li>
</ul>
</div>
<div id="license" class="section level2" number="1.3">
<h2><span class="header-section-number">1.3</span> License</h2>
<ul>
<li>MicrobioSee is under the MIT license. This tutorial is licensed under a Creative Commons Attribution 4.0 International License.</li>
<li>Update Time:20220301</li></ul>
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