This is some working code that pulls data from Tara Oceans and performs some analysis, generates some plots and data that can be output to cytoscape.
You need the following to get it to work:
R and RStudio
the following packages installed
install.packages("tidyverse"") # for plotting and wrangling data
install.packages("otuSummary"")
install.packages("reshape2") # has the melt function, which I use to wrangle data
install.packages("psych") # for calculating regular correlations with p values
You also need SpiekEasi, which requires install.packages(devtools)
install.packages(SpiecEasi) # Has sparcc and also does clr transforms
#library(devtools)
#install_github("zdk123/SpiecEasi")