label methods for cophylo plot

R/cophylo.R

@@ -44,8 +44,8 @@ cophylo<-function(tr1,tr2,assoc=NULL,rotate=TRUE,...){
 
 ## called internally by plot.cophylo to plot a phylogram
 ## written by Liam J. Revell
-phylogram<-function(tree,part=1,direction="right",fsize=1,ftype="i",lwd=1,...){
-	d<-if(direction=="right") 1 else -1
+phylogram<-function(tree,part=1,direction="rightwards",fsize=1,ftype="i",lwd=1,...){
+	d<-if(direction=="rightwards") 1 else -1
 	## check if edge lenths
 	if(is.null(tree$edge.length)) tree<-compute.brlen(tree)
 	## rescale tree so it fits in one half of the plot
@@ -87,6 +87,14 @@ phylogram<-function(tree,part=1,direction="right",fsize=1,ftype="i",lwd=1,...){
 			sub("_"," ",tree$tip.label[i]), pos=if(d<0) 4 else 2,offset=0,
 			cex=fsize,font=font)
 	}
+	PP<-list(type="phylogram",use.edge.length=TRUE,node.pos=1,
+		show.tip.label=if(ftype!="off") TRUE else FALSE,show.node.label=FALSE,
+		font=ftype,cex=fsize,adj=0,srt=0,no.margin=FALSE,label.offset=0,
+		x.lim=par()$usr[1:2],y.lim=par()$usr[3:4],
+		direction=direction,tip.color="black",Ntip=Ntip(cw),Nnode=cw$Nnode,
+		edge=cw$edge,xx=d*sapply(1:(Ntip(cw)+cw$Nnode),
+		function(x,y,z) y[match(x,z)],y=X,z=cw$edge),yy=y)
+	assign("last_plot.phylo",PP,envir=.PlotPhyloEnv)
 	## return rightmost or leftmost edge of tip labels
 	invisible(d*max(h+fsize*strwidth(tree$tip.label)))
 }
@@ -119,10 +127,13 @@ plot.cophylo<-function(x,...){
 	par(mar=mar)
 	plot.window(xlim=xlim,ylim=ylim)
 	x1<-phylogram(x$trees[[1]],part=0.4,...)
-	x2<-phylogram(x$trees[[2]],part=0.4,direction="left",...)
+	left<-get("last_plot.phylo",envir=.PlotPhyloEnv)
+	x2<-phylogram(x$trees[[2]],part=0.4,direction="leftwards",...)
+	right<-get("last_plot.phylo",envir=.PlotPhyloEnv)
 	if(!is.null(x$assoc)) makelinks(x,c(x1,x2))
 	else cat("No associations provided.\n")
 	if(any(scale.bar>0)) add.scalebar(x,scale.bar,fsize)
+	assign("last_plot.cophylo",list(left=left,right=right),envir=.PlotPhyloEnv)
 }
 
 ## add scale bar
@@ -183,3 +194,27 @@ tipRotate<-function(tree,x,...){
 	attr(tree,"minRotate")<-min(oo,pp)
 	tree
 }
+
+## labeling methods for plotted "cophylo" object
+## written by Liam J. Revell 2015
+
+nodelabels.cophylo<-function(...,which=c("left","right")){
+	obj<-get("last_plot.cophylo",envir=.PlotPhyloEnv)
+	if(which[1]=="left") assign("last_plot.phylo",obj[[1]],envir=.PlotPhyloEnv)
+	else if(which[1]=="right") assign("last_plot.phylo",obj[[2]],envir=.PlotPhyloEnv)
+	nodelabels(...)
+}
+
+edgelabels.cophylo<-function(...,which=c("left","right")){
+	obj<-get("last_plot.cophylo",envir=.PlotPhyloEnv)
+	if(which[1]=="left") assign("last_plot.phylo",obj[[1]],envir=.PlotPhyloEnv)
+	else if(which[1]=="right") assign("last_plot.phylo",obj[[2]],envir=.PlotPhyloEnv)
+	edgelabels(...)
+}
+
+tiplabels.cophylo<-function(...,which=c("left","right")){
+	obj<-get("last_plot.cophylo",envir=.PlotPhyloEnv)
+	if(which[1]=="left") assign("last_plot.phylo",obj[[1]],envir=.PlotPhyloEnv)
+	else if(which[1]=="right") assign("last_plot.phylo",obj[[2]],envir=.PlotPhyloEnv)
+	tiplabels(...)
+}