microbiota/amplicon

Statistics and visualization for amplicon data

R package "amplicon" for amplicon data statistics and visualization in microbiome

Statistics and visualization for amplicon data in microbiome

Examples of visualizations.

Main features:

• Input feature (OTU/ASV/Taxonomic) tables, metadata;
• Supports more than ten analysis methods, provides multiple visualization styles;
  • Alpha diversity: index barplot, boxplot with stat label;
  • Beta diveristy: Supported 47 distance * 8 ordination methods, output scatter plot with stat eclippse and sample label;
  • Taxonomic composition: Stackplot in samples or groups, even support bubble plot.
• Published-ready figures and tables.

Install

Please open RStudio， and run the following code for install.

library(devtools)
install_github("microbiota/amplicon")

Detail

You can used it following the vignettes, we recommended use it in EasyAmplicon

• EasyAmplicon: https://github.com/YongxinLiu/EasyAmplicon

Reference

If used this script, please cited:

Yong-Xin Liu, Lei Chen, Tengfei Ma, Xiaofang Li, Maosheng Zheng, Xin Zhou, Liang Chen, Xubo Qian, Jiao Xi, Hongye Lu, Huiluo Cao, Xiaoya Ma, Bian Bian, Pengfan Zhang, Jiqiu Wu, Ren-You Gan, Baolei Jia, Linyang Sun, Zhicheng Ju, Yunyun Gao, Tao Wen, Tong Chen. 2023. EasyAmplicon: An easy-to-use, open-source, reproducible, and community-based pipeline for amplicon data analysis in microbiome research. iMeta 2: e83. https://doi.org/10.1002/imt2.83

Copyright 2016-2023 Yong-Xin Liu [email protected], Tao Wen [email protected], Tong Chen [email protected]

amplicon's Issues

Sorry, but there are some wrong when i run your "format2lefse"

Thanks for all your work sincerely! That's a great achievement and it benefit me most. While when i run the code in R，there are some problem. The data i used to run code is come from yours.

#Warning message:
#Factor Kingdom contains implicit NA, consider using forcats::fct_explicit_na

so, i want to know whether you have time to solve my problem, thanks a lot!

alpha_rare_all error#no loop for break/next, jumping to top level

Hello!
I am running the code below which do not work. The pyseq and group should be fine, but when I try to make the plot it just runs forever and when I stopped it (forced it to stop) I got the error message: no loop for break/next, jumping to top level
Any idea of what is going on?

Greate pacakge!!
Maria

ara = alpha_rare_all(
ps = physeq,
method = "Richness",
group = "intervention")

R version error

i first used R3.6.3 to install it, but some errors showed it cant be installed. then i change r4.0.0 to install it, but the same error occured. what version r is suit to install it

tax_stackplot绘图问题

绘图时根据分组在X轴来排列样品，但是有的组中含有的样品较多，有的组较少。这种情况下绘制的图bar的宽度有大有小，导致图片不美观，同时也影响了空间的利用，即样品较多的组中bar非常细，导致看不清楚，而样品较少的组中bar非常宽，占用了很多空间，是否可以进行调整，使得bar的宽度一致，而分组的宽度随着组内样品的多少而自由伸缩？

R Error : (converted from warning) unable to re-encode 'BetaDiv.R' lines 120, 170, 201

> install_local("C://tempscp//amplicon-master.zip")
Installing package into ‘C:/Users/Wolvesled/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'amplicon' ...
** using staged installation
** R
Error : (converted from warning) unable to re-encode 'BetaDiv.R' lines 120, 170, 201
ERROR: unable to collate and parse R files for package 'amplicon'
* removing 'C:/Users/Wolvesled/Documents/R/win-library/4.0/amplicon'
Error: Failed to install 'amplicon-master.zip' from local:
  (converted from warning) installation of package ‘C:/Users/******/amplicon-master’ had non-zero exit status

seems encoding error at 'BetaDiv.R' lines 120, 170, 201

index赋值richness，shannon等以后显示error找不到

错误报告如下：

p = alpha_boxplot(alpha_div, index = shannon, metadata, groupID = "Back")
Error in [.data.frame(alpha_div, rownames(sampFile), index) :
object 'shannon' not found
p = alpha_boxplot(alpha_div, index = richness, metadata, groupID = "Back")
Error in [.data.frame(alpha_div, rownames(sampFile), index) :
object 'richness' not found

另外还有一个问题请教老师，就是原生R语言环境，采用R脚本运行，就是Rscript alpha_boxplot.R时弹出找不到对象p是怎么回事，把那句“p”的判断语句直接注释掉，又报错说找不到make_option函数

Package lacks integration with phyloseq

Hello, I've tried to use some basic functions provided within microbiota/amplicon, although they seem very interesting current lack of integration reading metadata or otu_table from phyloseq objects or biom itself hampers its usage.

One suggestion, in case the developer does not want to provide this integration, is to provide an example of the input files (i.e. alpha_boxplot tables obtained used usearch).

Best,