Hi @hpyle50,
The default is that all features are plotted (both significant and insignificant). You can provide a threshold by passing --p-significance-threshold. For example, if you provide --p-significance-threshold 0.01, it will only plot features that achieved a q-value less than or equal to 0.01.
(Note, just to avoid possible confusion: the p in --p-significance-threshold, indicates that this is a parameter to this visualizer, it's not indicating that this is a p-value significance threshold.)