Count the number of unique taxa represented by cluster(s) or sequences in phylota table Use rnk to specify a taxonomic level to count. If NULL counts will be made to the lowest level reported on NCBI.
Arguments
- phylota
Phylota object
- cid
Cluster ID(s)
- sid
Sequence ID(s)
- rnk
Taxonomic rank
- keep_higher
Keep higher taxonomic ranks?
See also
Other tools-public:
calc_mad(),
calc_wrdfrq(),
drop_by_rank(),
drop_clstrs(),
drop_sqs(),
get_clstr_slot(),
get_nsqs(),
get_sq_slot(),
get_stage_times(),
get_tx_slot(),
get_txids(),
is_txid_in_clstr(),
is_txid_in_sq(),
list_clstrrec_slots(),
list_ncbi_ranks(),
list_seqrec_slots(),
list_taxrec_slots(),
plot_phylota_pa(),
plot_phylota_treemap(),
read_phylota(),
write_sqs()
Examples
data('bromeliads')
# how many species are there?
(get_ntaxa(phylota = bromeliads, cid = '0', rnk = 'species'))
#> 0
#> 1050
# how many genera are there?
(get_ntaxa(phylota = bromeliads, cid = '0', rnk = 'genus'))
#> 0
#> 76
# how many families are there?
(get_ntaxa(phylota = bromeliads, cid = '0', rnk = 'family'))
#> 0
#> 1
# use list_ncbi_ranks() to see available rank names
(list_ncbi_ranks())
#> [1] "superkingdom" "kingdom" "phylum" "subphylum" "class"
#> [6] "superorder" "order" "suborder" "infraorder" "parvorder"
#> [11] "family" "genus" "species" "subspecies"