Quantification of Relative Abudance Data Generated From Metagenomic Sequencing
This is an .Rmarkdown script designed to take data generated from the cli tool GRAMMY, which estimates species relative abundances from a mixed community of bacteria using short-read sequencing data. This script takes the .csv produced by GRAMMY to create realtive abundance plots and calcuate the relative abudance of each species across replicates, communities, and an entire gradient of species richness. The origin of the data is from my chemostat experiment (which I will in the future link a description here).
Below is an area plot produced with the .Rmd script. It shows how all possible combinations of four bacterial species evolved in communities change through 184 generations of experimental evolution.
