Recreating maaslin2-generated graphs starting with raw data


I need to edit the graphs generated in the maaslin2 output, so I am looking to recreate them myself, starting with my raw data. The processing parameters that I entered when I ran maaslin2 included TSS normalization and log transformation. I can find and copy the log transformation performed by maaslin2, but am running into issues finding a function to perform TSS normalization. Is there a function that you would recommend to perform TSS normalization given a count OTU table?

Thank you for your input!


You can find the source code for the TSS normalization method here. You can see it’s calling vegan::decostand() under the hood if you want to try using that directly.

Thank you for your reply!