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 all_results.tsv Summary Plots 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
