col.edge.phylo: Coloring terminal branch of trees

In giby/Linarius: Linarius: A package for phylogeographic studies, with all functions that are missing in both phylogenetic and geographical packages

Description

Generate colors for terminal edge branch of a phylogenic tree

Usage

col.edge.phylo(phy, groups, color = c(2, 3, 4, 5), root.color = 1)

Arguments

phy	A tree of class phylo
groups	A vector indicating what should be of the same color
color	A vector indicating the color to choose
root.color	A single color, to use for non terminal edge

Note

This function should be used with the package ade4

See Also

ade4

Examples

data(Birch)
require(vegan)
require(ade4)
require(ape)
dist=vegdist(Betula, method="jaccard", binary=TRUE, diag=FALSE, upper=FALSE, na.rm = FALSE)
dendro=hclust(dist,"complete")
dendro2<-as.phylo(dendro,cex=0.5)
plot(dendro2,,type="u",lab4ut="axial",font=1, adj=1,label.offset = 0.01,edge.color = col.edge.phylo(dendro2,code$Ploidy),tip.color = code$Ploidy)

giby/Linarius documentation built on May 17, 2019, 4:20 a.m.