# This function creates a phylomorsphace plot of Sidlauskas (2006)
# Written by Liam J. Revell 2010
phylomorphospace<-function(tree,X,A,control=list()){
	
	# control list
	con=list(col.edge=matrix(data="black",nrow(tree$edge),1,dimnames=list(as.character(tree$edge[,2]),"color")),
		col.node=matrix(data="black",nrow(tree$edge),1,dimnames=list(as.character(tree$edge[,2]),"color")))
		
	con[(namc <- names(control))] <- control

	con$col.edge<-as.matrix(con$col.edge); con$col.node<-as.matrix(con$col.node)

	require(calibrate)

	plot(x=A[1,1],y=A[1,2],xlim=range(c(X[,1],A[,1])),ylim=range(c(X[,2],A[,2])),xlab=colnames(X)[1],ylab=colnames(X)[2])

	X<-X[tree$tip.label,]
	attach(tree); if(!exists("node.label")) tree$node.label<-as.character(length(tree$tip.label)+1:tree$Nnode); detach(tree)
	tree$node.label<-as.character(tree$node.label)
	A<-A[tree$node.label,]

	X<-rbind(X,A)

	for(i in 1:nrow(tree$edge)){
		lines(x=c(X[tree$edge[i,1],1],X[tree$edge[i,2],1]),y=c(X[tree$edge[i,1],2],X[tree$edge[i,2],2]),col=con$col.edge[as.character(tree$edge[i,2]),1])
		# lines(x=c(X[tree$edge[i,1],1],X[tree$edge[i,2],1]),y=c(X[tree$edge[i,1],2],X[tree$edge[i,2],2]))
		points(x=c(X[tree$edge[i,1],1],X[tree$edge[i,2],1]),y=c(X[tree$edge[i,1],2],X[tree$edge[i,2],2]),col=con$col.node[as.character(tree$edge[i,2]),1])
		#points(x=c(X[tree$edge[i,1],1],X[tree$edge[i,2],1]),y=c(X[tree$edge[i,1],2],X[tree$edge[i,2],2]))
		if(tree$edge[i,2]<=length(tree$tip.label))
			textxy(X=X[tree$edge[i,2],1],Y=X[tree$edge[i,2],2],labs=tree$tip.label[tree$edge[i,2]],cx=0.75)		
	}

}