plot_phylota_pa: Plot presence/absence matrix

Description Usage Arguments Details Value See Also Examples

View source: R/user-special.R

Description

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

Usage

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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

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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

phylotaR documentation built on July 31, 2018, 5:01 p.m.