plotAbundance problem

[antagomir]

The function plotAbundance is used for handy visualization of community composition.

library(mia)
data(GlobalPatterns)
tse <- GlobalPatterns[1:1000,]
plotAbundance(tse, abund_values="counts", rank = "Phylum")

It only works with the defined ranks, however. This leads to error:

rowData(tse)$Strain <- sample(letters[1:5], nrow(tse), replace=TRUE)
plotAbundance(tse, abund_values="counts", rank = "Strain")

-> Error: 'rank' must be a value from 'taxonomyRanks()'

This is restrictive because it is often useful to visualize also other types of groupings.

Just not providing the rank argument (relying on the default) did not seem to help either.

Is this intended, or is there a way to circumvent this issue?

Related to microbiome/mia#219

[antagomir]

Related to microbiome/mia#325 also

[TuomasBorman]

Yes, the grouping could be more general (just a column from rowData)

[antagomir]

Related to #132