taxonomizr (version 0.10.6)

makeNewick: Create a Newick tree from taxonomy

Description

Create a Newick formatted tree from a data.frame of taxonomic assignments

Usage

makeNewick(
  taxa,
  naSub = "_",
  excludeTerminalNAs = FALSE,
  quote = NULL,
  terminator = ";"
)

Value

a string giving a Newick formatted tree

Arguments

taxa

a matrix with a row for each leaf of the tree and a column for each taxonomic classification e.g. the output from getTaxonomy

naSub

a character string to substitute in place of NAs in the taxonomy

excludeTerminalNAs

If TRUE then do not output nodes downstream of the last named taxonomic level in a row

quote

If not NULL then wrap all entries with this character

terminator

If not NULL then add this character to the end of the tree

See Also

getTaxonomy

Examples

taxa<-matrix(c('A','A','A','B','B','C','D','D','E','F','G','H'),nrow=3)
makeNewick(taxa)
taxa<-matrix(c('A','A','A','B',NA,'C','D','D',NA,'F','G',NA),nrow=3)
makeNewick(taxa)
makeNewick(taxa,excludeTerminalNAs=TRUE)
makeNewick(taxa,quote="'")