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

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

Value

geom_object

Details

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

See also

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