plot_clade: Function to plot clades extracted from the backbone...

In iramosgutierrez/randtip: A generalized framework to expand incomplete phylogenies with taxonomic information

Function to plot clades extracted from the backbone phylogeny.

Description

Function to plot clades extracted from the backbone phylogeny.

Usage

plot_clade(
  get.clade.out,
  ppcr.col = "#4a8a21",
  nonppcr.col = "#48bce0",
  unknown.col = "#adadad",
  ...
)

Arguments

get.clade.out	Output of the get_clade function (a phylogenetic clade)
ppcr.col	Color for the tips representing species placed in the specified taxonomic group (default is green).
nonppcr.col	Color for the tips representing other species but those placed in the specified taxonomic groupnt clade (default is blue).
unknown.col	Color for the tips representing species without taxonomic information (default is grey).
...	Further arguments to pass through plot.phylo function.

Value

Less inclusive clade that includes all the species in the specified taxonomic group.

Author(s)

Ignacio Ramos-Gutierrez, Rafael Molina-Venegas, Herlander Lima

Examples

catspecies <- c("Lynx_lynx", "Panthera_uncia",
"Panthera_onca", "Felis_catus", "Puma_concolor",
"Lynx_canadensis", "Panthera_tigris", "Panthera_leo",
"Felis_silvestris")

cats.info <- build_info(species=catspecies, tree= cats,
     find.ranks=TRUE, db="ncbi", mode="backbone")

felinae.clade <- get_clade(info=cats.info,
tree=cats, group="Felinae")

plot_clade(felinae.clade, ppcr.col="green",
nonppcr.col="red",unknown.col="grey" )

iramosgutierrez/randtip documentation built on March 19, 2024, 6:35 p.m.