One of the best features of LEfSe in my opinion was the simplicity of the output illustration. With MaAsLin, there does not seem to be an equivalent. I’ve generated a boxplot with all significant features, but it is much less clear than the LDA score plot that comes from LEfSe. Is there any alternative approach to representing significant features identified by MaAsLin that is readily digestable akin to the LEfSe output?
The most equivalent plot that can be generated from Maaslin2 would be the heatmap showing strengths of coefficients for significant features. Unfortunately there is nothing that quite replicates the LDA plot that LEFSe generates but you could create a similar plot using custom code and the coefficients of each feature with the metadata of interest.
We really appreciate the feedback and will include more visualization options in Maaslin going forward including something more akin to LEfSe output.