LEfSe analysis, plotting negative LDA score (log10)

I want to plot LDA score with negative and positive likeCapture

where should I need to change the parameter?

Hi Shaminur,

I am not really sure what you are asking. Do you have results where you have found negative and positive associations but you are only getting the LEfSe plot in one of those directions? For a standard two-variable factor you should receive a plot like the one you posted (from the plot_res.py command) if you have both positive and negative associations. I believe if you go up to three factors then it adds a third color and makes everything one direction, but I certainly could be wrong about that.

A similar answer was posted here (with a bit more detail): LDA score treatment comparison: All treatments in one table or separate table for each treatment?