spiral_phylo: Draw phylogenetic tree

In spiralize: Visualize Data on Spirals

Draw phylogenetic tree

Description

Draw phylogenetic tree

Usage

spiral_phylo(
  obj,
  gp = gpar(),
  log = FALSE,
  reverse = FALSE,
  group = NULL,
  group_col = NULL,
  track_index = current_track_index()
)

phylo_to_dendrogram(obj, log = FALSE)

Arguments

obj	A stats::dendrogram object.
gp	Graphical parameters of the tree edges, mainly as a global setting.
log	Whether the height of the tree to be log-transformed log10(x + 1)?
reverse	Whether the tree to be reversed?
group	A categorical variable for splitting the tree.
group_col	A named vector which contains group colors.
track_index	Index of the track.

Details

phylo_to_dendrogram() converts a phylo object to a dendrogram object.

The motivation is that phylogenetic tree may contain polytomies, which means at a certain node, there are more than two children branches. Available tools that do the conversion only support binary trees.

The returned dendrogram object is not in its standard format which means it can not be properly drawn by the stats::plot.dendrogram() function. However, you can still apply stats::cutree() to the returned dendrogram object with no problem and the dendrogram can be properly drawn with the ComplexHeatmap package (see examples).

Value

Height of the phylogenetic tree.

A stats::dendrogram object.

Examples

if(require(ape)) {
    data(bird.families)
    n = length(bird.families$tip.label)
    spiral_initialize(xlim = c(0, n), start = 360, end = 360*3)
    spiral_track(height = 0.8)
    spiral_phylo(bird.families)
}
if(require(ape)) {
    data(bird.families)
    d = phylo_to_dendrogram(bird.families)

    ComplexHeatmap::grid.dendrogram(d, test = TRUE)
}

spiralize documentation built on June 22, 2024, 10:45 a.m.