update to plot.cophylo method to permit different font sizes for the …

…two trees

R/cophylo.R

@@ -124,13 +124,18 @@ plot.cophylo<-function(x,...){
 	else scale.bar<-rep(0,2)
 	if(hasArg(ylim)) ylim<-list(...)$ylim
 	else ylim<-if(any(scale.bar>0)) c(-0.1,1) else c(0,1)
-	if(hasArg(fsize)) fsize<-list(...)$fsize
-	else fsize<-1
+	obj<-list(...)
 	par(mar=mar)
 	plot.window(xlim=xlim,ylim=ylim)
-	x1<-phylogram(x$trees[[1]],part=0.4,...)
+	leftArgs<-rightArgs<-obj
+	if(!is.null(obj$fsize)&&length(obj$fsize)>1){
+		leftArgs$fsize<-obj$fsize[1]
+		rightArgs$fsize<-obj$fsize[2]
+	}
+	x1<-do.call("phylogram",c(list(tree=x$trees[[1]],part=0.4),leftArgs))
 	left<-get("last_plot.phylo",envir=.PlotPhyloEnv)
-	x2<-phylogram(x$trees[[2]],part=0.4,direction="leftwards",...)
+	x2<-do.call("phylogram",c(list(tree=x$trees[[2]],part=0.4,
+		direction="leftwards"),rightArgs))
 	right<-get("last_plot.phylo",envir=.PlotPhyloEnv)
 	if(!is.null(x$assoc)) makelinks(x,c(x1,x2))
 	else cat("No associations provided.\n")