EasyMicroPlot package aims to provide an easy-to-use microbiome analysis tool on R platform that accomplishes the core tasks of metagenomic down-stream analysis from start to finish, specially designed by screening popular microbial analysis and visualization metric in recent clinic studies.

if(! require("devtools")) install.packages("devtools")
library(devtools)
install_github("xielab2017/EasyMicroPlot",subdir='Version_0.5.0')
# When something is wrong, please try this below
install_github("xielab2017/EasyMicroPlot",subdir='Version_0.5.0',upgrade = 'never')

• vegan (>= 2.5-6)
• ape (>= 5.3)
• grid (>= 3.5.1)
• plyr (>= 1.8.6)
• dplyr (>= 1.0.2)
• multcomp (>= 1.4-14)
• patchwork (>= 1.0.1)
• fs (>= 1.5.0)
• stringr (>= 1.4.0)
• htmlwidgets (>= 1.5.3)
• ggiraph (>= 0.7.0)
• ggpubr (>= 0.4.0)
• ggplot2
• randomForest (>= 4.6-14)
• purrr (>= 0.3.4)
• reshape2 (>= 1.4.4)
• psych (>= 2.0.12)
• IM (>= 5.1.1)
• table1 (>= 1.4.2)
• pROC (>= 1.17.0.1)
• orrplot (>= 0.84)
• igraph (>= 1.2.6)
• filesstrings (>= 3.2.1)
• grid (>= 3.6.3)
• ggrepel (>= 0.9.1)
• RColorBrewer(>= 1.1-2)
• scales(>= 1.1.1)

When mapping and microbial relative abundance filies have already been deposited in working directory,
users could activate easy mode to perform a complete workflow with default parameters and generate results in workspace.
Demo data at this repository: Tutorial data/Easy_mode_data.7z

EMP_MICRO()

./Result
├── RFCV_result
│   ├── Imprortance
│   ├── model
│   └── taxonomy
├── alpha_result
│   ├── Post-Hoc
│   ├── data
│   ├── html
│   └── pic
├── beta_result
│   ├── bray_0.001_0.7
│   └── jaccard_0.001_0.7
├── cooc_result
│   └── pic
├── core_data
│   ├── species_0.001_70%.txt
│   └── species_0.001_70%_info.txt
└── structure_result
    ├── pic
    ├── taxonomy
    └── top_abundance

More feature and tutorial is below :
https://github.com/xielab2017/EasyMicroPlot/wiki

If you use EMP in published research, please cite this article:

EasyMicroPlot : An Efficient and Convenient R Package in Microbiome Downstream Analysis and Visualization for Clinical Study.

1. (2021) Susu Zhang #, Peili Wu #, Ye Tian#, Bingdong Liu#, Liujing Huang , Zhihong Liu, Nie Lin , Ningning Xu, Yuting Ruan, Zhen Zhang, Ming Wang, Zongbing Cui, HongWei Zhou, Liwei Xie, Hong Chen, Jia SunGut Microbiota Serves a Predictable Outcome of Short-Term Low-Carbohydrate Diet (LCD) Intervention for Patients with Obesity. Microbiol. Spectr.

2. (2021) Liujing Huang#, Bingdong Liu#, Zhihong Liu, Wanqin Feng, Minjuan Liu, Yifeng Wang, Dongxian Peng, Xiafei Fu, Honglei Zhu, Zongbin Cui, Liwei Xie ,Ying Ma Gut Microbiota Exceeds Cervical Microbiota for Early Diagnosis of Endometriosis. Frontiers Cellular and Infection Microbiology

3. (2022) Limin Xu*, Bingdong Liu*, Liujing Huang*, Ze Li*, Yanbo Cheng, Ye Tian, Guihua Pan, Huijun Li ,Yinlan Xu, Weidong Wu, Zongbin Cui, Liwei Xie Probiotic consortia and their metabolites ameliorate the symptoms of inflammatory bowel diseases in a colitis mouse model. Microbiol. Spectr.