These files were used to create the plots for the paper "Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria" by Kelly Wyres and Kathryn Holt.

Each directory contains: 
- data downloaded from public databases NCBI (genomes) and IMNGS (microbiomes) in March 2018 (sources given in each file); and 
- R code to run on the data files to generate Figures 2 & 3 in the paper.

Required packages: ggplot2, reshape2, grid, Rmisc