Clone and run the following commands:
export PYTHONPATH=$PYTHONPATH:$PWD
cd ./agplots/
./scripts/make_plots.py -m data/AGSr123_raw_8.28.13_fixed.txt -t data/our_filtering_97PI_trimmed_rare1000_L2.txt -c 'SIMPLE_MATTER' -v 'FECAL' -s data/sample_labels.txt -o out_ -k data/key_taxa.txt