View source: R/phylomorphospace.R
phylomorphospace | R Documentation |
Project a phylogeny into morphospace.
phylomorphospace(tree, X, A=NULL, label=c("radial","horizontal","off"),
control=list(), ...)
project.phylomorphospace(tree, X, nsteps=200, sleep=0,
direction=c("to","from","both"), ...)
tree |
a phylogenetic tree in |
X |
an |
A |
an optional |
label |
string indicating whether to plot the tip labels in the same direction as the terminal edge ( |
control |
a list containing the following optional control parameters: |
nsteps |
for |
sleep |
for |
direction |
for |
... |
optional arguments for plotting, including |
This function creates a phylomorphospace plot (a projection of the tree into morphospace) for two characters following Sidlauskas (2008; Evolution). It will also plot a discrete character mapped on tree.
project.phylomorphospace
animates the phylomorphospace projection.
This function creates a phylomorphospace plot
Liam Revell liam.revell@umb.edu
Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-90.
Revell, L. J. (2014) Graphical methods for visualizing comparative data on phylogenies. Chapter 4 in Modern phylogenetic comparative methods and their application in evolutionary biology: Concepts and practice (L. Z. Garamszegi ed.), pp. 77-103.
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
Sidlauskas, B. (2008) Continuous and arrested morphological diversification in sister clades of characiform fishes: A phylomorphospace approach. Evolution, 62, 3135-3156.
## load tree & data from Revell & Collar (2009)
data(sunfish.tree)
data(sunfish.data)
## set colors for mapped discrete character
cols<-setNames(c("blue","red"),
levels(sunfish.data$feeding.mode))
phylomorphospace(sunfish.tree,sunfish.data[,3:2],
colors=cols,bty="l",ftype="off",node.by.map=TRUE,
node.size=c(0,1.2),xlab="relative buccal length",
ylab="relative gape width")
title(main="Phylomorphospace of buccal morphology in Centrarchidae",
font.main=3)
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