Hi !

I am discovering the MaAsLin2 package.

I am doing a comparison of the metagenome of healthy volunteers (named CT) versus patients (named AML) using R and the latest release version of Maaslin2 (updated this morning). I would like to have the plots with the CT placed in the first column and the AML placed in the second column.

I followed the instructions found here.

https://huttenhower.sph.harvard.edu/maaslin/

Setting reference levels

But despite having the factors set at the right level, the output is still not correct.

Here are my R lines

mapping_T0$Group_ordered = factor(mapping_T0$Group, levels=c(â€śCTâ€ť,â€śAMLâ€ť))

fit_data = Maaslin2(input_data = data.filter2, input_metadata = mapping_T0, output = â€śMaaslin2_with_filtersâ€ť, fixed_effects = c(â€śGroup_orderedâ€ť))

str(mapping_T0$Group_ordered)

Factor w/ 2 levels â€śCTâ€ť,â€śAMLâ€ť: 2 2 2 2 2 2 2 2 2 2 â€¦

I saw the reference option here GitHub - biobakery/Maaslin2: MaAsLin2: Microbiome Multivariate Association with Linear Models and here Reference values for a categorical fixed effect variable but it seems to work only with factors of more than 2 levels.

I looked at similar posts, and didnâ€™t find a solution. I hope I didnâ€™t miss it.

Thanks for your input !

Looking forward to learning more about the package