Focal clades

Clades of interest to be plotted in color

Usage

focalClade(Tibble, left, right, color, displayName)

Arguments

Tibble

A ConvenientTblTree object.

left, right

Leaf labels whose most common recent ancestor will define the clade

color

Color of the clade in plots

displayName

Display name of the clade (can contain spaces)

See also

Other Focal clade functions: eog(), recordAncestor(), recordClades(), subTree(), visualizeTree()

Examples

(Halobacterium <- focalClade(Halo_Tree,
  "Halobacterium_noricense", "Halobacterium_salinarum", "blue", "Halobacterium genus"))
#> Halobacterium genus, node ID: 10, number of genomes: 3
(Haloferax <- focalClade(Halo_Tree,
  "Haloferax_mediterranei", "Haloferax_volcanii", "green3", "Haloferax genus"))
#> Haloferax genus, node ID: 8, number of genomes: 2
(clades <- FocalCladeList(Halobacterium, Haloferax))
#> Halobacterium genus, node ID: 10, number of genomes: 3
#> Haloferax genus, node ID: 8, number of genomes: 2
visualizeTree(Halo_Tree) + clades