# function to plot special types of phylogeny visualizations
# so far the only implemented type is "extinction" in which all branches leading to extinct taxa (or prior to the MRCA of extant species)
# are plotted with red dashed lines
# written by Liam J. Revell 2012

fancyTree<-function(tree,type=c("extinction","traitgram3d"),...,control=list()){
	if(class(tree)!="phylo") warning("tree should be an object of class 'phylo'")
	if(type=="extinction") extinctionTree(tree)
	if(type=="traitgram3d") traitgram3d(tree,X,control)
}

# extinctionTree internal function
# written by Liam J. Revell 2012

extinctionTree<-function(tree){
	edges<-rep(0,nrow(tree$edge))
	names(edges)<-tree$edge[,2]
	extant<-getExtant(tree)
	ca<-findMRCA(tree,extant)
	root.node<-length(tree$tip)+1
	if(ca!=root.node){
		z<-setdiff(Descendants(tree,root.node,type="all"),Descendants(tree,ca,type="all"))
		edges[as.character(z)]<-1
	}
	z<-Descendants(tree,ca,type="all")
	y<-Descendants(tree,z)
	for(i in 1:length(z)) if(!any(tree$tip.label[y[[i]]]%in%extant)) edges[as.character(z[i])]<-1
	plot.phylo(tree,edge.color=edges+1,edge.lty=edges+1,edge.width=2,no.margin=TRUE)
}

# traitgram3d internal function
# written by Liam J. Revell 2012

traitgram3d<-function(tree,X,control){
	A<-apply(X,2,function(x,tree) anc.ML(tree,x)$ace,tree=tree)
	if(is.null(colnames(X))) colnames(X)<-c("x","y")
	X<-cbind(X,diag(vcv(tree))[rownames(X)])
	A<-cbind(A,nodeHeights(tree)[match(rownames(A)[1:nrow(A)],tree$edge)])
	colnames(X)[3]<-colnames(A)[3]<-"time"
	phylomorphospace3d(tree,X,A,control=control)
}