plot.graphclust: Plot phylogenetically constrained clustering

In phylosignal: Exploring the Phylogenetic Signal in Continuous Traits

Plot phylogenetically constrained clustering

Description

This function produces three plots (selectable by which): a plot of edges selection based on phylogenetic against trait distances of taxa pairs, a plot of the graph produced with the selected edges and a plot of the clustered phylogenetic tree.

Usage

## S3 method for class 'graphclust'
plot(
  x,
  which = c("selection", "graph", "tree"),
  ask = TRUE,
  colored = TRUE,
  ...
)

Arguments

x	a graphclust object as produced by graphClust.
which	a character vector to select plots. Must be one or more of "selection", "graph", "tree".
ask	logical if TRUE (default), the user is asked before each plot.
colored	logical indicating if plots must include colors.
...	further arguments to be passed to or from other methods. They are currently ignored in this function.

Examples

data(navic)
gC <- graphClust(navic, lim.phylo = 1, lim.trait = 2, scale.lim = FALSE)
plot.graphclust(gC, which = "selection", ask = FALSE)
plot.graphclust(gC, which = "graph", ask = FALSE)
plot.graphclust(gC, which = "tree", ask = FALSE)

phylosignal documentation built on Oct. 12, 2023, 5:13 p.m.