Hi there,
Thanks for your question and apologies for the delayed response!! The reduction in the number of features presented here I don’t think is Wilcoxon test- you had the same number of features before and after. That is what the 340 (340) indicated, I believe. The reduction is selected for the most significant figures using an LDA score above 2. That reduces your number of discriminative features to 219. However, as has been noted Wilcoxon is still run by default even in the absence of subclasses (see: Lefse without any subclass- still valid?). You can specify this in the command line version as said in the that post.
I’m not sure I followed your middle question about the subclasses, where you interested in using a subclass in your analysis?
The LDA finds features that discriminate one class from the another class. I.e. if any class is significantly different from all other classes, it will be reported. The plotted score is the highest in all such comparisons. It does not say anything about comparisons among other classes. Does that make sense?
I hope this helps!
Best,
Kelsey