Thanks for all of the help you provide. Really thankful.
I worked on my feature table in R for visualisations.
I can see a difference when I visualise after filtering (outside qiime2) between top taxa and top certain taxa (ex: genera).
So I was wondering why is this happening?
In the case of top taxa, I use the whole table subset of the top 10 taxa while in the case of the top genus, I aggregate or glom the taxa to a certain level (genus in this case) and then subset and plot. Also, I do the same for top species, where I aggregate or glom the taxa to a certain level (species in this case) and then subset and plot.
here are some examples of the plots
So I can see that there is a top genus; Flavobacterium
Not necessarily true. If there is no species label for Flavobacterium. Then it will be dropped when you filter at the species level, because the species label is NA. Which may be the reason why it does not appear in the species plot.
Alternatively... many species of Flavobacterium are combined together when grouping at the genus-level... but individually each member species is not enough to register at the top for the species level. Thus, looking at top species will effectively resort compared to top genera, etc...