Count number of unique taxa

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.

Usage

get_ntaxa(phylota, cid = NULL, sid = NULL, rnk = NULL, keep_higher = FALSE)

Arguments

phylota

Phylota object

cid

Cluster ID(s)

sid

Sequence ID(s)

rnk

Taxonomic rank

keep_higher

Keep higher taxonomic ranks?

Value

vector

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"