MakeEdgeLabels: Creates Edge Labels for Hierarchy Trees

Description

These functions will create edge labels for hierarchy trees.

Usage

getTipList(phy)
whichEdge(phy, taxa)
node.leaves(phy, node)
node.offspring(phy, node)
WhatToDoWithDuplicateEdgeNames(edgeLabels, duplicateEdgeLabels)
MakeEdgeLabels(MyHiers, label="all", missingData=NULL, duplicateEdgeLabels="oldest")

Arguments

phy

A tree in the class phylo

node

Any node number in the tree

MyHiers

A vector of hier pages OR a list of XMLs as an R object

taxa

Vector of tip taxa

edgeLabels

Vector of edge labels with the same associated branch

duplicateEdgeLabels

Choice of which edge label to prefer: recent, oldest, or combined

missingData

If tip taxa are not all the same taxonomic rank, should Reol cleave out taxa or hierarchical rank first

label

Which hierarchical units should be included in the edge labels

Value

MakeEdgeLabels returns a vector of edges and their clade names to be used in apes edgeLabels function. getTipList, WhatToDoWithDuplicateEdgeNames, and whichEdge are internal functions for MakeEdgeLabel.

Details

Note that edges are slightly different than node labels, in that edges are plotted along the center of the branch rather than at a node. Plotting both is redundant, but one or the other may look better aesthetically. Also edges in the edgeLabels function is not the actual edge number, but the row. Our functions reflect this. There will likely be cases where edges have more than one hierarchical name (for example, the branch to camel species will have the genus Camelus and the family Camelidae). When making edge labels, you have the choice of using the most recent hierarchical name (genus in the camel example) or the oldest (family in camels), or you can choose to combine the names so that you can see all of them (Camilidae.Camelus).

Examples

Run this code

library(ape)
data(MyHiers)
Tree <- MakeHierarchyTree(MyHiers, includeNodeLabels=FALSE)
edges <- MakeEdgeLabels(MyHiers)	
plot(Tree, show.node.label=FALSE)
edgelabels(text=names(edges), edge=edges)  


## Not run: 
# edges <- MakeEdgeLabels(MyHiers, missingData="pruneTaxa", duplicateEdgeLabels="recent")
# plot(Tree, show.node.label=FALSE)
# edgelabels(text=names(edges), edge=edges)  
# ## End(Not run)