metaphlan_to_phyloseq() now no longer requires data to be pre-filtered to a chosen taxonomic rank when not directly loading from a file.
Taxonomic rank is now optional for metaphlan_to_phyloseq() and deactivated by default, i.e. taxa_lvl = NULL, suppressing the filtering. Simply specify a valid taxonomic rank with taxa_lvl to filter to this rank.
Added support for Species Genome Bin (SGB) as an additional taxonomic rank (set taxa_lvl = 't').
metaphlanToPhyloseq 0.1.0
shorten_clade_names() now also works with data that wasn’t pre-filtered to a chosen taxonomic rank, returning the taxon without rank prefix for the chosen rank as before, and the last taxon with rank prefix for all others for clarity and as a reminder that data was not filtered to a specific taxonomic rank.
The planned feature, which would have made it possible to load metadata directly from a path in metaphlan_to_phyloseq(), was discarded due to the large number of file formats in which metadata can be available.
Fixed valid taxonomic rank check for cases in which ‘order’ was written out.