BIEN_phylogeny_label_nodes {BIEN}

Label nodes on a phylogeny

Description

BIEN_phylogeny_label_nodes will label the nodes on a phylogeny based on either the BIEN taxonomy or user-supplied taxa.

Usage

BIEN_phylogeny_label_nodes(
  phylogeny,
  family = TRUE,
  genus = FALSE,
  other_taxa = NULL,
  ...
)

Arguments

phylogeny

A single phylogeny.

family

Should family-level nodes be labeled? Default is TRUE.

genus

Should genus-level nodes be labeled? Default is FALSE. Overwrites family-level nodes where a family contains a single genera.

other_taxa

A dataframe containing two columns: 1) the taxa to be labelled; 2) the species associated with each taxon.

...

Additional arguments passed to internal functions.

Value

Input phylogeny with labeled nodes.

Note

Information on the construction of the BIEN phylogenies is available online at https://bien.nceas.ucsb.edu/bien/biendata/bien-2/phylogeny/

See Also

Other phylogeny functions: BIEN_phylogeny_complete(), BIEN_phylogeny_conservative()

Examples

## Not run: 
phylogeny<-BIEN_phylogeny_conservative()

phylogeny<-drop.tip(phy = phylogeny,tip = 101:length(phylogeny$tip.label))
plot.phylo(x = phylogeny,show.tip.label = FALSE)

fam_nodes<-BIEN_phylogeny_label_nodes(phylogeny = phylogeny,family = TRUE)
plot.phylo(x = fam_nodes,show.tip.label = FALSE, show.node.label = TRUE)

gen_nodes<-BIEN_phylogeny_label_nodes(phylogeny = phylogeny, family = FALSE, genus = TRUE)
plot.phylo(x = gen_nodes, show.tip.label = FALSE, show.node.label = TRUE)

other_taxa <- as.data.frame(matrix(nrow = 10,ncol = 2))
colnames(other_taxa)<-c("taxon","species")
other_taxa$taxon[1:5]<-"A" #Randomly assign a few species to taxon A
other_taxa$taxon[6:10]<-"B" #Randomly assign a few species to taxon B
tax_nodes <- 
 BIEN_phylogeny_label_nodes(phylogeny = phylogeny,
                            family = FALSE, genus = FALSE, other_taxa = other_taxa)
plot.phylo(x = tax_nodes,show.tip.label = FALSE,show.node.label = TRUE)
## End(Not run)