MicrobiotaProcess for GPA vs RA vs control

https://bioconductor.org/packages/release/bioc/vignettes/MicrobiotaProcess/inst/doc//MicrobiotaProcess.html

1. prepare the R environment

   #Rscript MicrobiotaProcess.R
   #NOTE: exit R script, then login again R-environment; rm -rf Phyloseq*_cache
   
   # -- using R under base environment --
   #(base) jhuang@WS-2290C:~/DATA_A/Data_Nicole8_Lamprecht_new_PUBLISHED/core_diversity_e1300
   #mkdir figures
   rmarkdown::render('Phyloseq.Rmd',output_file='Phyloseq.html')
   

2. bridges other tools

   ##https://github.com/YuLab-SMU/MicrobiotaProcess
   ##https://www.bioconductor.org/packages/release/bioc/vignettes/MicrobiotaProcess/inst/doc/MicrobiotaProcess.html
   ##https://chiliubio.github.io/microeco_tutorial/intro.html#framework
   ##https://yiluheihei.github.io/microbiomeMarker/reference/plot_cladogram.html
   #BiocManager::install("MicrobiotaProcess")
   #install.packages("microeco")
   #install.packages("ggalluvial")
   #install.packages("ggh4x")
   library(MicrobiotaProcess)
   library(microeco)
   library(ggalluvial)
   library(ggh4x)
   library(gghalves)
   library(tidyr)
   

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