Sarela Garcia-Santamarina, Michael Kuhn, Saravanan Devendran, Lisa Maier, Marja Driessen, André Mateus, Eleonora Mastrorilli, Ana Rita Brochado, Mikhail M. Savitski, Kiran R Patil, Michael Zimmermann, Peer Bork, Athanasios Typas
This repository contains all code to generate the main and supplementary figures from the pre-processed data. (Pre-processing includes: determining relative species abundances from 16S sequencing data, determining AUCs from growth curves, processing metabolomics data.) All preprocessed data is in the data folder. Statistical analyses and figures are all in R, and can be invoked on the shell using the Makefile (make). pacman is used to load and, if necessary, install missing packages.
make will generate the figures in PNG format. make TIFF converts the PNGs to TIFFs needed for journal submission, using ImageMagick.