plot_phylota_pa: Plot presence/absence matrix

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Plot presence/absence matrix

Description

Plot presence/absence of taxa by each cluster in phylota object.

Usage

plot_phylota_pa(phylota, cids, txids, cnms = cids, txnms = txids)

Arguments

phylota	Phylota object
cids	Vector of cluster IDs
txids	Vector of taxonomic IDs
cnms	Cluster names
txnms	Taxonomic names

Details

Cluster names and taxonomic names can be given to the function, by default IDs are used.

Value

geom_object

See Also

Other tools-public: calc_mad(), calc_wrdfrq(), drop_by_rank(), drop_clstrs(), drop_sqs(), get_clstr_slot(), get_nsqs(), get_ntaxa(), 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_treemap(), read_phylota(), write_sqs()

Examples

library(phylotaR)
data(cycads)
# drop all but first ten
cycads <- drop_clstrs(cycads, cycads@cids[1:10])
# plot all
p <- plot_phylota_pa(phylota = cycads, cids = cycads@cids, txids = cycads@txids)
print(p)  # lots of information, difficult to interpret
# get genus-level taxonomic names
genus_txids <- get_txids(cycads, txids = cycads@txids, rnk = 'genus')
genus_txids <- unique(genus_txids)
# dropping missing
genus_txids <- genus_txids[genus_txids !=  '']
genus_nms <- get_tx_slot(cycads, genus_txids, slt_nm = 'scnm')
# make alphabetical for plotting
genus_nms <- sort(genus_nms, decreasing = TRUE)
# generate geom_object
p <- plot_phylota_pa(phylota = cycads, cids = cycads@cids, txids = genus_txids,
                     txnms = genus_nms)
# plot
print(p)  # easier to interpret

ropensci/phylotaR documentation built on July 9, 2023, 3:17 p.m.