plot_phylota_pa: Plot presence/absence matrix
In phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Description Usage Arguments Details Value See Also Examples

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

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

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

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

geom_object

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

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