Prevalence at higher taxonomical level than species

[AgnesBaud]

Describe the bug

At species level, we get:

But at genus level, we get:

Expected behavior

We should have Staphylococcus, Streptococcus etc. at 100%.

Explanation

This is because in the code we do the mean of the prevalence of the species of the genus (prev_ser_taxa = self.prevalence_series.groupby(taxa_level).mean()) instead of doing the prevalence on the dataframe grouped by genus.

[AgnesBaud]

Temporary trick to bypass that bug is to give the dataframe already grouped at the "genus" level to the plotting class:

from moonstone.plot import PlotTaxonomyCounts
ins = PlotTaxonomyCounts(count_df.groupby("genus").sum())
fig = ins.plot_most_prevalent_taxa(taxa_level="genus")