Usage:

STEP 1: Generate lefse like results using maaslin3

Rscript lefse_testing.R \
    --input hmp_aerobiosis_small.txt \
    --normalize FALSE \
    --class oxygen_availability \
    --random_component subject_id

Output

lefse_style_results_abundance.res
lefse_style_results_prevalence.res

STEP2: Generating lefse like plots

lefse_plot_res.py lefse_style_results_prevalence.res hmp_prevalance_aerobiosis_small.png

lefse_plot_res.py lefse_style_results_abundance.res hmp_abundance_aerobiosis_small.png

STEP3: Generating lefse like cladogram

lefse_plot_cladogram.py lefse_style_results_prevalence.res hmp_prevalence_aerobiosis_small.cladogram.png --format png

lefse_plot_cladogram.py lefse_style_results_abundance.res hmp_abundance_aerobiosis_small.cladogram.png --format png