I am trying to analyse some data with LEfSe on anaconda (python).
I successfully execute the script with the example data
Is the cladogram supposed to look like this? If so, how can I change the colors for the biomarkers? If not, I believe it is because no biomarker clade was found (I could not generate the other picture (step 3, see below)).
The code I run is the following:
bin/format_input.py tmp/sample.txt tmp/merged_abundance_table.lefse
bin/run_lefse.py tmp/merged_abundance_table.lefse tmp/merged_abundance_table.lefse.out -l 4
bin/plot_res.py --dpi 300 tmp/merged_abundance_table.lefse.out output_images/lefse_biomarkers.png
bin/plot_res.py --dpi 300 tmp/merged_abundance_table.lefse.out tmp/lefse_biomarkers.png
I am not sure about the format_input.py parameters (-c,-s,-u,-o) what do they do? Online I could not find any info and the code where they are used is not commented so, before trying to back-engineer everything I am glad to ask.