Open antagomir opened 2 years ago
The function plotAbundance is used for handy visualization of community composition.
plotAbundance
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.
rank
Is this intended, or is there a way to circumvent this issue?
Related to microbiome/mia#219
Related to microbiome/mia#325 also
Yes, the grouping could be more general (just a column from rowData)
Related to #132
The function
plotAbundance
is used for handy visualization of community composition.It only works with the defined ranks, however. This leads to error:
-> 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