# function plots a tree; in the new version this is just a wrapper for plotSimmap # written by Liam Revell 2012, 2013 plotTree<-function(tree,...){ if(hasArg(color)) color<-list(...)$color else color<-NULL if(hasArg(fsize)) fsize<-list(...)$fsize else fsize<-1.0 if(hasArg(ftype)) ftype<-list(...)$ftype else ftype<-"reg" if(hasArg(lwd)) lwd<-list(...)$lwd else lwd<-2 if(hasArg(pts)) pts<-list(...)$pts else pts<-FALSE if(hasArg(node.numbers)) node.numbers<-list(...)$node.numbers else node.numbers<-FALSE if(hasArg(mar)) mar<-list(...)$mar else mar<-NULL if(hasArg(add)) add<-list(...)$add else add<-FALSE if(hasArg(offset)) offset<-list(...)$offset else offset<-NULL if(hasArg(type)) type<-list(...)$type else type<-"phylogram" if(hasArg(direction)) direction<-list(...)$direction else direction<-"rightwards" if(class(tree)=="multiPhylo"){ par(ask=TRUE) if(!is.null(color)) names(color)<-"1" for(i in 1:length(tree)) plotTree(tree[[i]],color=color,fsize=fsize,ftype=ftype,lwd=lwd,pts=pts,node.numbers=node.numbers,mar=mar,add=add,offset=offset,direction=direction,type=type) } else { tree$maps<-as.list(tree$edge.length) for(i in 1:length(tree$maps)) names(tree$maps[[i]])<-c("1") if(!is.null(color)) names(color)<-"1" plotSimmap(tree,colors=color,fsize=fsize,ftype=ftype,lwd=lwd,pts=pts,node.numbers=node.numbers,mar=mar,add=add,offset=offset,direction=direction,type=type) } }