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Interpretation and visualization of microbiome charts

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MicrobiomeStatPlot 微生物组数据分析与可视化 (Microbiome data analysis and visualization)

0.项目简介 (Introduction)

高通量测序的发展极大地推动了微生物组/宏基因组领域的发展。微生物组的数据分析和解读需要微生物学、生物信息学、统计学、Shell和R语言、宏基因组学等多学科的知识，无论是中国还是世界范围内仍缺少系统的学习教材。宏基因组公众号成立的目的是打破微生物组数据分析解读的壁垒，推动本领域的发展。目前经常三年的积累，已发布数百篇本领域相关数据分析、可视化和科研经验的教程。但本领域发展迅速，很多教程需要更新，而且团队成员的知识和研究领域有限，需要更广泛的同行加入，打造宏基因组学入门百科全书，现向全球华人圈全面征集《微生物组数据分析与可视化实战》章节编写的创作者和审稿人。

The development of high-throughput sequencing has greatly promoted the development of the microbiome/metagenomics field. The data analysis and interpretation of the microbiome requires multidisciplinary knowledge such as microbiology, bioinformatics, statistics, Shell and R language, metagenomics, etc. There is still a lack of systematic learning materials both in China and around the world. The purpose of establishing the "Metagenome" Public WeChat Account is to break the barriers to the analysis and interpretation of microbiome data and promote the development of this field. At present, with three years of accumulation, hundreds of tutorials on data analysis, visualization and scientific research experience in this field have been published. However, this field is developing rapidly, many tutorials need to be updated, and the knowledge and research fields of team members are limited. A wider range of peers need to join in to create an introductory encyclopedia of metagenomics. Now we are comprehensively soliciting authors and reviewers of the chapter "Microbiome Data Analysis and Visualization Practice" from the global Chinese community.

创始人就是你，赶快加入贡献你的智慧吧！

You are the founder, join us now and contribute your wisdom!

创作者要求 (Creator requirements)

  • 本领域的专业同行，专业包括且不限于微生物学、生物信息学、微生物组学，或应用培养组学、扩增子、宏基因组、宏转录组、宏病毒组、宏蛋白组、宏代谢组、宏表观组等技术研究人类、动植物、环境的相关研究人员(年级和职称不限)；
  • Professional colleagues in this field, including but not limited to microbiology, bioinformatics, microbiome, or researchers who use culturomics, amplicon, metagenomics, macrotranscriptomics, macrovirome, macroproteomics, macrometabolomics, macroepigenetics and other technologies to study humans, animals, plants, and the environment (without restrictions on grade and title);
  • 有专业知识搜集和整理的能力，有记录电子笔记、发表文章经历者的优先；
  • Those who have the ability to collect and organize professional knowledge, and have experience in recording electronic notes and publishing articles are preferred;
  • 认领下方目录中章节，按照参考模板(一周内陆续发布前几节样章)，采用有道云笔记markdown格式或Rmarkdown(加入后有免费培训)编写逻辑严谨、考虑读者感受、可重复性强的教程；
  • Claim the chapters in the directory below, follow the reference template (the first few sample chapters will be released within a week), use Youdao Cloud Notes markdown format or Rmarkdown (free training after joining) to write a logically rigorous, reader-friendly, and repeatable tutorial;
  • 对宏基因组编辑部提出的合理意见进行认真修改；
  • Carefully revise the reasonable suggestions made by the Metagenome Editorial Department;

创作者福利（Creator benefits）

  • 创作者作为章节的作者之一；
  • The creator is one of the authors of the chapter;
  • 结识宏基因组核心团队成员，见习编辑可获取编辑的基础培训；
  • Get to know the core members of the metagenomics team, and trainee editors can get basic training in editing;
  • 发布文章三篇或过万字，可成为正式编辑，免费获得价值万元的最新扩增子、宏基因组分析流程或参加培训、会议的机会；
  • Publish three articles or more than 10,000 words to become a formal editor, and get the latest amplicon and metagenomic analysis process worth 10,000 yuan for free, or participate in training and conferences.
  • 相关教程、技术文档可推荐发表SCI论文，详见：《JoVE微生物组专刊征稿，写方法拍视频教程发SCI》
  • Related tutorials and technical documents can be recommended for publishing SCI papers, see: "JoVE Microbiome Special Issue Call for Papers, Write Methods, Shoot Video Tutorials, and Publish SCI"
  • 根据贡献，获得团队发表论文、出版图书的署名权；
  • Based on your contribution, you will get the right to publish papers and books by your team;

审稿人要求（Reviewer requirements）

  • 专业审稿人，建议有发表文章经历，对自己擅长领域章节的逻辑、语言的全面修改和提出改进建议(同论文审稿)；
  • Professional reviewers, who are recommended to have experience in publishing articles, will comprehensively revise the logic and language of the chapters in their areas of expertise and make suggestions for improvement** (same as paper review);
  • 大众审稿人，对公众号发布文章中可改进地方提出意见或建议，可通过文章下方留言、联系公众号管理员等方式沟通；
  • Public reviewers, who can make comments or suggestions on areas for improvement in articles published by the public account**, can communicate by leaving a message below the article or contacting the public account administrator;

审稿人福利（Reviewer benefits）

  • 专业审稿人可进入编辑部，作为审核文章的责任编辑，获得责编栏姓名和单位的署名权；
  • Professional reviewers can join the editorial department and serve as responsible editors for reviewing articles, and obtain the right to sign their names and units in the responsible editor column;
  • 大众审稿人的姓名和单位可出现在章节的致谢部分；
  • The names and affiliations of public reviewers may appear in the chapter acknowledgments;
  • 审稿人节日福利红包！
  • Holiday bonus for reviewers!

联系宏基因组公众号 (Contact Metagenome WeChat Public Account)

创作者和审稿人任务登记： https://kdocs.cn/l/c7CGfv9Xc

Creator and reviewer task registration: https://kdocs.cn/l/c7CGfv9Xc 宏基因组创作者和审稿人登记表.xlsx，使用微信登陆金山文档，登记姓名、单位、研究方向、职称、负责章节具体分工等信息

Registration form for metagenome authors and reviewers.xlsx, use WeChat to log in to Kingsoft Document, register name, unit, research direction, title, specific division of labor in charge of chapters, etc.

联系人：白德凤 / 刘永鑫

Contact: Defeng Bai / Yong-Xin Liu

微信(WeChat)：baidefeng1234win / meta-genomics

广告营销人员较多，添加微信务必备注姓名-单位-职位-研究方向，否则无法通过好友申请

There are many advertising and marketing personnel. When adding WeChat, please be sure to indicate your name, unit, position, and research direction. Otherwise, your friend request will not be accepted.

邮箱(Email)：[email protected] / [email protected]

目前整理本领域基础知识、常用分析、必备技能的目录。部分章节有前期发布的资源和教程供参考。有自己擅长章节的作者，欢迎认领相应章节进行更新或从头创作。如果你觉得有自己擅长而且重要的知识和方法，欢迎联系我们一起讨论目录的更新。

At present, we have organized the catalog of basic knowledge, common analysis, and essential skills in this field. Some chapters have previously released resources and tutorials for reference. Authors who have chapters they are good at are welcome to claim the corresponding chapters for update or creation from scratch. If you think you have knowledge and methods that you are good at and important, please contact us to discuss the update of the catalog.

中文的宏基因组学百科全书期待你的贡献！

The Chinese Encyclopedia of Metagenomics awaits your contribution!

推荐序 (Recommendations)

找在本领域积累多年的专家、学者，如朱永官院士、蓝灿辉总裁、赵方庆研究员、王军研究员、褚海燕研究员、韦中教授等对本书进行点评。

We will find experts and scholars with many years of experience in this field, such as Academician Zhu Yongguan, President Lan Canhui, Researcher Zhao Fangqing, Researcher Wang Jun, Researcher Chu Haiyan, Professor Wei Zhong, etc. to comment on this book.

编者序（Editor's Preface）

你能学到什么、近年来技术发展概述和展望。

What you can learn, an overview of technological developments in recent years and prospects.

1.生物信息与微生物组 (Bioinformatic and microbiome)

1.1 生物信息概述 (Overview of bioinformatics)

1.1.1 实验设计和元数据 (Study design and metadata)

1.1.2 分析的基本思路 (Basic idea pf analysis)

1.2 Shell和Linux (Shell and Linux tutorials)

1.3 R统计与绘图 (Statistics and plotting using R)

1.3.1 R语言基础 (R language basics)

1.3.2 ggplot2绘图基础 (ggplot2 drawing basics)

1.3.3 R语言绘图专辑 (R language drawing album)

1.3.4 高级统计绘图 (Advanced statistical graphics)

1.4 Python数据处理和绘图 (Python data processing and plotting)

1.5 微生物组概述 (Microbiome overview)

发展史：摸索，初步探索，建立方法，百花齐放。

Development history: groping, initial exploration, establishing methods, and letting a hundred flowers bloom.

测序平台和数据

Sequencing platform and data

常用研究手段(Common research methods)

1.5.1 培养组 (Culturome)

1.5.2 扩增子16S (Amplicon 16S)

1.5.3 宏基因组 (Metagenomics)

1.5.4 其他宏组学 (Other meta-omics)

真菌组 18S/ITS (Fungal 18S/ITS)

功能基因 (Functional genes)

代谢组 (Metabolome)

基因组 (Genome)

转录组 (Transcriptome)

有时研究也会涉及宿主、微生物的基因表达研究。更多转录组、单细胞的文章可关注生信宝典公众号。

Sometimes the research also involves the study of gene expression of hosts and microorganisms. For more articles on transcriptomes and single cells, please follow the Bioinformatics Guide WeChat public account.

2.微生物组分析流程(原始数据到特征表) (Microbiome analysis pipelines)

盘点主流软件。高级阶段应该是各种方法步骤的自由组合，甚至是根据需要设计、开发方法。

Take stock of mainstream software. The advanced stage should be a free combination of various methods and steps, or even design and develop methods according to needs.

2.1 培养组 (Culturome)

2.2 扩增子 (Amplicon)

格式转换 (Format coversion)

2.2.1 USEARCH/VSEARCH

2.2.2 QIIME 2

2.3 宏基因组 (Metagenomics)

2.3.1 有参分析Read-based (Read-based analysis)

2.3.2 无参Assembly-based (Assemble-based analysis)

2.3.3 功能注释数据库 (Functional annotation database)

2.3.4 分箱专题 (Binning)

2.4 认识特征表 Feature table

特征表是上游大数据分析的终点，是里程碑式的成果，同时也是下游分析的起始。

3.特征表的统计、可视化和解读 (Visualization and interpretation)

3.1 统计学基础 (Basic statistics)

3.1.1 正态性检验和方差齐性分析 (Normality test and analysis of variance homogeneity)

3.1.2 t检验、方差分析、卡方检验使用注意事项 (Notes on using t-test, ANOVA, and chi-square test)

3.1.3 两组和多组秩和检验 (Two-group and multiple-group rank sum test)

3.1.4 多重比较的P值校正 (P value correction for multiple comparisons)

3.1.5 物种数据标准化方法和注意事项 (Species data standardization methods and considerations)

3.2 Alpha多样性 (Alpha diversity)

3.2.1 箱线图或柱状图 (Box plots and bar plots)

3.2.2 稀释曲线 (Rare curve)

3.2.3 维恩图 (Venn)

维恩图的变形，如UpsetView，网络图等。

Variations of Venn diagrams, such as UpsetView, network diagrams, etc.

3.3 Beta多样性 (Beta diversity)

3.3.1 非限制性排序 PCoA/NMDS

  1. 主成分分析PCA
  2. 主坐标分析PCoA
  3. 非度量多维尺度分析NMDS
  4. 对应分析CA
  5. 其他排序pls-da，opls-da，t-sne

3.3.2 统计方法 PERMANOVA

  1. PERMANOVA
  2. ANOSIM
  3. MRPP

3.3.3 限制性排序 (Constrained sorting)

  1. 限制性主坐标分析Constrained PCoA
  2. 冗余分析RDA
  3. 典范对应分析CCA
  1. LDA

3.4 物种组成 (Species composition)

3.4.1 堆叠柱状图 (Stacked bar plot)

3.4.2 弦图 (Chord plot)

3.4.3 树图/气泡图 (Tree plot/Bubble plot)

3.5 差异比较 (Differential analysis)

3.5.1 t检验和秩和检验 (t-test and rank-sum test)

3.5.2 负二项分布和计数型差异分析 (Negative binomial distribution and count variance analysis) edgeR/DESeq2

  1. 什么是物种数据的过度离散现象和负二项分布
  2. 用edgeR包进行差异分析
  3. DESeq2包进行差异分析

3.5.3 STAMP与扩展柱状图 (STAMP and extended bar chart)

3.5.4 LEfSe和Cladogram

3.5.5 其他常用差异分析方法 (Other commonly used difference analysis methods)

  1. ANCOM分析
  2. ALDEx2分析
  3. songbird和DEICODE介绍
  4. limma

3.6 网络分析 (Network analysis)

3.6.1 网络基础知识 (Network basics)

3.6.2 可视化入门 (Visualization introduction)

  1. 按分类或模块着色网络 (Coloring networks by categories or modules)
  2. 网络属性 (Network properties)
  3. 全局属性 (Global properties)
  4. 节点属性 (Nodes properties)

3.6.3 可视化进阶 (Advanced visualization)

  1. 双网络比对 (Dual network comparison)
  2. 多网络时间序列 (Multi-network time series)
  3. Gephi美化 （Gephi beautification）

3.7 机器学习 （Machine learning）

3.7.1 机器学习的常用算法 (Common algorithms for machine learning)

3.7.2 随机森林分类 (Random forest classification)

黄适：这个RandomForest package 非常慢，已经完全不适应大数据分析需求。推荐使用ranger https://github.com/imbs-hl/ranger

  1. 分类
  2. 分类评估-ROC曲线及DCA分析

3.7.3 随机森林回归 (Random forest regression)

  1. 回归
  2. 回归及效果评价

3.7.4 Adaboost/slime2

3.7.5 深度学习 (Deep learning)

3.7.6 来源追溯SourceTracker/FEAST

3.7.7 其他常用算法 (Other commonly used algorithms)

  1. 人工神经网络分类 (Artificial neural network classification)
  2. 支持向量机分类 (Support vector machine classification)
  3. 逻辑回归（GLM）(Logistic regression)

3.8 树形图 (Phylogenetic tree)

3.8.1 进化树构建 (Phylogenetic tree construction)

  1. 多序列比对
  2. 建树Fastree/RaxL
  3. 宏基因组中建树Phylophlan3
  4. iTOL美化进化树
  5. ggtree美化进化树

3.8.2 分类树构建 (Classification tree construction)

  1. Graphlan与Cladogram
  2. Krona
  3. Metacoder

3.9 相关分析 (Correlation analysis)

3.9.1 特征与环境因子相关 (Traits and environmental factors correlations)

3.9.2 特征间相关(同网络) (Correlation between features)

3.9.3 相关分析的可视化 (Visualization of correlation analysis)

4. 文章套路总结 (Routine and ideas)

4.1 扩增子 (Amplicon)

4.2 宏基因组 (Metagenome)

4.2.1 参考基因集 (Reference genomes)

4.2.2 碳水化合物 (Carbohydrate)

4.2.3 抗生素抗性 (Antibiotic resistance)

4.3 扩增子+宏基因组 (Amplicon and metagenome)

4.4 其他研究热点 (Other research hotspots)

  • 人类：肠型、肥胖、二型糖尿病、IBD、早产、关联分析
  • 动物：无菌小鼠、牛瘤胃、食性、宿主和微生物共进化
  • 植物：根际、叶际、代谢物、氮利用、抗病
  • 环境：抗生素耐药、抗生素挖掘、极端环境、生命之树

5. 附录 (Appendix)

5.1 实验设计 (Study design)

实验方案，样本元数据收集，样本名命名规则和示例。

Experimental protocol, sample metadata collection, sample naming conventions and examples.

5.2 测序平台和测序技术 (Sequencing platform and technology)

5.3 数据备份与发布 (Data backup and release)

NCBI，GSA，EBI

5.4 图片排版和美化 (Image layout and beautification)

5.5 杂志点评 (Journal comments)

CNS，Microbiome，ISME

相关文章按杂志分类

5.6 论文写作、投稿和文献整理 (Paper writing, submission and literature compilation)

5.7 机遇与挑战 (Opportunities and challenges)

目前的优缺点和不足，未来的发展方向。

Current advantages, disadvantages and shortcomings, and future development directions.

5.8 三代测序 (Next-generation sequencing)

NBT的PacBio和ONT文章简介

NBT's PacBio and ONT article introduction

5.9 经验和资源推荐 (Experience and resource recommendations)

经验 (Experience)

办工效率 (Work efficiency)

书籍专著 (Books and monographs)

国外教程 (Foreign tutorial)

5.10 宏基因组精品文章(专题) (Metagenomics featured articles) (Special topic)

本书主要参考文献全文解读

网站数据库 (Online database)

软件算法和流程 (Software algorithms and pipelines)

方法评测 (Method evaluation)

培养组 (Culturome)

肠型 (Enterotype)

基金 (Funds)

人物传记 (Biography)

参考基因(组)集 (Reference genomes)

病毒组 (Viromics)

5.11 猜你喜欢 (You may also like)

写在后面 (Write at the back)

为鼓励读者交流、快速解决科研困难，我们建立了“宏基因组”专业讨论群，目前己有国内外5000+ 一线科研人员加入。参与讨论，获得专业解答，欢迎分享此文至朋友圈，并扫码加主编好友带你入群，务必备注“姓名-单位-研究方向-职称/年级”。技术问题寻求帮助，首先阅读《如何优雅的提问》学习解决问题思路，仍末解决群内讨论，问题不私聊，帮助同行。

To encourage readers to communicate and quickly solve scientific research difficulties, we have established a "Metagenomics" professional discussion group, which has more than 5,000 frontline researchers at home and abroad. To participate in the discussion and get professional answers, please share this article with your friends and scan the code to add the editor-in-chief to join the group. Be sure to note "name-unit-research direction-professional title/grade". To seek help with technical problems, first read "How to Ask Elegant Questions" to learn how to solve problems. If you still have not solved the problem, discuss it in the group. Don't chat privately about the problem. Help your peers. image

学习扩增子、宏基因组科研思路和分析实战，关注“宏基因组”

Learn about amplicon and metagenomic research ideas and analysis practices, and focus on "metagenomics" image

image

点击阅读原文，跳转最新文章目录阅读

Click to read the original text and jump to the latest article directory https://mp.weixin.qq.com/s/5jQspEvH5_4Xmart22gjMA

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