Usage:

STEP 1: Generate lefse like results using maaslin3

Rscript maaslin3_lite.R    \
 --input hmp_aerobiosis_small.txt   \
 --normalize FALSE    \
 --class oxygen_availability   \
 --subclass body_site  \   
 --random_component subject_id    \ 
 --alpha_threshold 0.1

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