arc_labels: Add arc labels to plotted phylogeny

In phyloregion: Biogeographic Regionalization and Macroecology

Add arc labels to plotted phylogeny

Description

Add arc labels to plotted phylogeny

Usage

arc_labels(phy, tips, ...)

## Default S3 method:
arc_labels(
  phy = NULL,
  tips,
  text,
  plot_singletons = TRUE,
  ln.offset = 1.02,
  lab.offset = 1.06,
  cex = 1,
  orientation = "horizontal",
  ...
)

Arguments

phy	An object of class phylo.
tips	A character vector (or a list) with names of the tips that belong to the clade or group. If multiple groups are to be plotted, tips must be given in the form of a list.
...	Further arguments passed to or from other methods.
text	Desired clade label.
plot_singletons	Logical. If TRUE (default), adds arcs (and labels) to single tip lineages. If FALSE, no arc or labels will be plotted over that tip..
ln.offset	Line offset (as a function of total tree height)
lab.offset	Label offset.
cex	Character expansion
orientation	Orientation of the text. Can be “vertical”, “horizontal”, or “curved”.

Value

NULL

Examples

old.par <- par(no.readonly = TRUE)
require(ape)
data(africa)
par(mai=rep(0,4))
plot(africa$phylo, type = "fan", show.tip.label=FALSE,
     open.angle = 180, edge.width=0.5)

y <- data.frame(species=africa$phylo$tip.label)
y$genus <- gsub("_.*", "\\1", y$species)

fx <- split(y, f=y$genus)

suppressWarnings(invisible(lapply(fx, function(x) {
  y <- seq(from = 1.03, to = 1.09, by = ((1.09 - 1.03)/(length(fx) - 1)))
  z <- sample(y, 1, replace = FALSE, prob = NULL)
  if(nrow(x) > 10L) arc_labels(phy = africa$phylo, tips=x$species,
                            text=as.character(unique(x$genus)),
                            orientation = "curved", cex=0.5,
                            lab.offset = z)
})))
par(old.par)

phyloregion documentation built on Aug. 15, 2023, 9:07 a.m.