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easymicroplot's Introduction

EasyMicroPlot: An Efficient and Convenient R package in Microbiome DownStream Analysis and Visualization for Clinical Study

Awesome

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.

INSTALLATION

Github

install.packages('remotes')
remotes::install_github("https://github.com/xielab2017/EasyMicroPlot",subdir='Version_0.5')

Gitee
Make sure git tool on your computer installed correctly.

install.packages('remotes')
remotes::install_git("https://gitee.com/xielab2017/EasyMicroPlot/",subdir='Version_0.5')

USAGE and Tutorial

Version update

  • 0.5.1.25
  1. Fix a bug in EMP_COR_SANKEY when modifying the edge colour
  • 0.5.1.24
  1. Fix the method parameter of adonis2 in the betaplot function.
  • 0.5.1.23
  1. Add Student's t-test and ellipse function for beta_plot moudle.

  2. Add cex.axis parameter to fix display error for meta_summary

  3. Fix some bugs.

Next update

The next version will be a giant change, and we will rebuild the EMP package for more exciting features.

  • Introduce tidyverse grammar into analysis process
  • Integate omics data into EMP package
  • Design more interactive function for new beginers
  • Add more beautiful design for figures

HOW TO CITE

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

Bingdong Liu, Liujing Huang, Zhihong Liu, Xiaohan Pan, Zongbing Cui, Jiyang Pan, Liwei Xie. EasyMicroPlot : An Efficient and Convenient R Package in Microbiome Downstream Analysis and Visualization for Clinical Study. Frontiers in Genetics. doi: 10.3389/fgene.2021.803627

easymicroplot's People

Contributors

liubingdong avatar xielab2017 avatar

Stargazers

 avatar Guo BaoBei avatar  avatar Zihao Duan avatar  avatar  avatar Jielong Huang avatar  avatar  avatar  avatar  avatar Xiaoping Li avatar  avatar 飞走的纸飞机 avatar Joshua avatar Cynthia Chibani avatar Jiwon Kim avatar Dave avatar Ben avatar Ahmed A Shibl avatar Chi Liu avatar

Watchers

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easymicroplot's Issues

Something is wrong: 选择了未定义的列

Hi Liubingdong,

When running 'EMP_MICRO(micro,mapping)', there is an alert emerging as "Something is wring : 选择了未定义的列".
The object 'micro' is as the attached file "micro.csv"; the object 'mapping' is as the attached "mapping.csv".

Could you please reproduce it, and see if there is something wrong?

Thanks :-)
micro.csv
mapping.csv

Can not install

install_github("xielab2017/EasyMicroPlot",subdir='Version_0.5.0')
Downloading GitHub repo xielab2017/EasyMicroPlot@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
cannot open URL 'https://api.github.com/repos/xielab2017/EasyMicroPlot/tarball/HEAD'
install_github("xielab2017/EasyMicroPlot",subdir='Version_0.5.0',upgrade = 'never')
Downloading GitHub repo xielab2017/EasyMicroPlot@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
cannot open URL 'https://api.github.com/repos/xielab2017/EasyMicroPlot/tarball/HEAD'


Above is the problem I encounted. Could you please figure out how to fix it?
Many thanks in advance! :-)

Data format

Hi,
Can you please provide more information on how users data should be imported for EasyMicroPlot to use.
I have currently just imported a csv file for my metadata and a csv file for the read counts of each taxa/samples
Thank you,
Emily

核心过滤模块

我在使用core_data <- data_filter(dir = '16s_data/',design = 'mapping/mapping.txt',min_relative = 0.001,min_ratio = 0.7,pattern='L7')时。出现:
Error in vec_as_location():
! ... must be empty.
x Problematic argument:

  • call = call
    Run rlang::last_error() to see where the error occurred.
    QQ截图20221107153022

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