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(), subMatrix(), subTree(), visualizeTree()

Author

Charles Plessy

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
#> Warning: `aes_()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`
#> ℹ The deprecated feature was likely used in the ggtree package.
#>   Please report the issue at <https://github.com/YuLab-SMU/ggtree/issues>.
#> Warning: Arguments in `...` must be used.
#> ✖ Problematic arguments:
#> • as.Date = as.Date
#> • yscale_mapping = yscale_mapping
#> • hang = hang
#> ℹ Did you misspell an argument name?
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the ggtree package.
#>   Please report the issue at <https://github.com/YuLab-SMU/ggtree/issues>.