Manipulating Maaslin2 Graphs

Hello - I have been using Maaslin2 to compare gut microbiota between my txt and sex groups. I am really happy with the results so far, but I don’t like the way the visualizations are coming out. For one, the order of my groups on the x axis is wrong, and I don’t know how to reorder them. I also would like to change the colors similar to what I can do in ggplot2. Is this doable in Maaslin2 or do I need to get the data out and put it directly into ggplot2 to have these options? Where can I find the final data that I would put in ggplot2 to recreate the graphs I am seeing from Maaslin2’s output (i.e., in the figures folder)? Is this the fitted.rds object? I would appreciate any advice! Thanks!

Also, what should I do if I have two reference groups? I have a treatment condition (VEH vs MOR) and sex (M vs F). VEH M is what I have set the reference group as, but Maaslin2 only calculates significant differences of each group (VEH F, MOR M, and MOR F) vs. VEH M. I also know whether the other groups differ (i.e, MOR M vs MOR F). Can I set two reference groups? Alternatively, can I repeat the same analysis with varying reference groups?