updates to dotTree to label trait columns

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: phytools
-Version: 0.6-63
-Date: 2018-11-9
+Version: 0.6-64
+Date: 2018-11-21
 Title: Phylogenetic Tools for Comparative Biology (and Other Things)
 Author: Liam J. Revell
 Maintainer: Liam J. Revell <liam.revell@umb.edu>
@@ -13,6 +13,6 @@ ZipData: no
 Description: A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes a diverse array of methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.
 License: GPL (>= 2)
 URL: http://github.com/liamrevell/phytools
-Packaged: 2018-11-9 12:00:00 EST
+Packaged: 2018-11-21 12:00:00 EST
 Repository: 
-Date/Publication: 2018-11-9 12:00:00 EST
+Date/Publication: 2018-11-21 12:00:00 EST

R/dotTree.R

@@ -1,5 +1,5 @@
 ## function to plot a tree with dots/circles for a plotted phenotype
-## written by Liam J. Revell 2016, 2017
+## written by Liam J. Revell 2016, 2017, 2018
 
 dotTree<-function(tree,x,legend=TRUE,method="plotTree",standardize=FALSE,...){
 	if(is.data.frame(x)) x<-as.matrix(x)
@@ -30,7 +30,8 @@ dotTree.continuous<-function(tree,x,color,legend,method,standardize,...){
 		else x<-x[,1]
 	}
 	if(hasArg(fsize)) fsize<-list(...)$fsize
-	else fsize<-1
+	else fsize<-c(1,0.8)
+	if(length(fsize)==1) fsize<-rep(fsize,2)
 	if(hasArg(x.space)) x.space<-list(...)$x.space
 	else x.space<-0.1
 	if(hasArg(k)) k<-list(...)$k
@@ -50,6 +51,7 @@ dotTree.continuous<-function(tree,x,color,legend,method,standardize,...){
 	max.x<-max(x)
 	if(any(x<0)) x<-x-min(x)
 	if(method=="plotTree"){
+		fsize<-fsize[1]
 		x<-x[tree$tip.label]
 		## plot tree
 		plotTree(tree,offset=1.7,ylim=c(-Ntip(tree)/25,
@@ -75,11 +77,18 @@ dotTree.continuous<-function(tree,x,color,legend,method,standardize,...){
 	} else if(method=="phylogram"){
 		if(is.vector(x)) x<-as.matrix(x)
 		x[]<-x[tree$tip.label,]
+		if(hasArg(mar)) mar<-list(...)$mar
+		else mar<-rep(0.1,4)
+		if(hasArg(xlim)) xlim<-list(...)$xlim
+		else xlim<-c(-0.5,0.55+x.space*ncol(x)+x.space/2)
+		if(hasArg(labels)) labels<-list(...)$labels
+		else labels<-FALSE
+		if(hasArg(ylim)) ylim<-list(...)$ylim
+		else ylim<-c(if(legend) -0.1 else 0,if(labels) 1.1 else 1)
 		## plot tree
 		plot.new()
-		par(mar=rep(0.1,4))
-		plot.window(xlim=c(-0.5,0.55+x.space*ncol(x)+x.space/2),
-			ylim=c(if(legend) -0.1 else 0,1))
+		par(mar=mar)
+		plot.window(xlim=xlim,ylim=ylim)
 		h<-phylogram(tree,...)
 		## get last phylo plot parameters
 		obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
@@ -88,20 +97,23 @@ dotTree.continuous<-function(tree,x,color,legend,method,standardize,...){
 		## plot points
 		rr<-(k*x/max(x)+x.space)/2*diff(par()$usr[1:2])/diff(par()$usr[3:4])/
 			(Ntip(tree)-1)
-		if(k<=0.8&&any(rr>(strwidth("W")*fsize/2))) 
-			rr<-rr/max(rr)*strwidth("W")*fsize/2
+		if(k<=0.8&&any(rr>(strwidth("W")*fsize[1]/2))) 
+			rr<-rr/max(rr)*strwidth("W")*fsize[1]/2
 		for(i in 1:ncol(x)){
 			nulo<-mapply(draw.circle,x=x.tip+1.2*strwidth("W")+x.space*(i-1),
 				y=y.tip,radius=rr[,i],MoreArgs=list(nv=200,col=color))
-			## draw.circle(x.tip+1.2*strwidth("W")+x.space*(i-1),y.tip,
-			##	nv=200,radius=rr[,i],col=color)
 		}
 		## add legend
 		if(legend){ 
 			h<-dot.legend(x=-0.45,y=-0.04,min.x,max.x,Ntip=Ntip(tree),
 				method="phylogram",...)
 			if(standardize) text(h,-0.04,"(SD units)",pos=4)
 		}
+		if(labels){
+			text(x=seq(max(x.tip)+1.2*strwidth("W"),
+				max(x.tip)+1.2*strwidth("W")+x.space*(ncol(x)-1),by=x.space),
+				y=rep(1.02,ncol(x)),colnames(x),srt=70,adj=c(0,0.5),cex=fsize[2])
+		}
 	}
 }
 
@@ -112,7 +124,8 @@ dotTree.discrete<-function(tree,x,color,legend,method,...){
 		else x<-x[,1]
 	}
 	if(hasArg(fsize)) fsize<-list(...)$fsize
-	else fsize<-1
+	else fsize<-c(1,0.8)
+	if(length(fsize)==1) fsize<-rep(fsize,2)
 	if(hasArg(x.space)) x.space<-list(...)$x.space
 	else x.space<-0.1
 	## reorder tree
@@ -140,11 +153,18 @@ dotTree.discrete<-function(tree,x,color,legend,method,...){
 	} else if(method=="phylogram"){
 		if(is.vector(x)) x<-as.matrix(x)
 		x[]<-x[tree$tip.label,]
+		if(hasArg(mar)) mar<-list(...)$mar
+		else mar<-rep(0.1,4)
+		if(hasArg(xlim)) xlim<-list(...)$xlim
+		else xlim<-c(-0.5,0.55+x.space*ncol(x)+x.space/2)
+		if(hasArg(labels)) labels<-list(...)$labels
+		else labels<-FALSE
+		if(hasArg(ylim)) ylim<-list(...)$ylim
+		else ylim<-c(if(legend) -0.1 else 0,if(labels) 1.1 else 1)
 		## plot tree
 		plot.new()
-		par(mar=rep(0.1,4))
-		plot.window(xlim=c(-0.5,0.55+x.space*ncol(x)+x.space/2),
-			ylim=c(if(legend) -0.06 else 0,1))
+		par(mar=mar)
+		plot.window(xlim=xlim,ylim=ylim)
 		h<-phylogram(tree,...)
 		## get last phylo plot parameters
 		obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
@@ -157,14 +177,17 @@ dotTree.discrete<-function(tree,x,color,legend,method,...){
 			nulo<-mapply(draw.circle,x=x.tip+1.2*strwidth("W")+x.space*(i-1),
 				y=y.tip,col=color[as.character(x[,i])],MoreArgs=list(nv=20,
 				radius=r))
-			## draw.circle(x.tip+1.2*strwidth("W")+x.space*(i-1),y.tip,
-			##	nv=200,radius=r,col=color[as.character(x[,i])])
 		}
 		## add legend
 		if(legend){ 
 			add.simmap.legend(colors=color,prompt=FALSE,
 				vertical=FALSE,shape="circle",x=-0.45,y=-0.06)
 		}
+		if(labels){
+			text(x=seq(max(x.tip)+1.2*strwidth("W"),
+				max(x.tip)+1.2*strwidth("W")+x.space*(ncol(x)-1),by=x.space),
+				y=rep(1.02,ncol(x)),colnames(x),srt=70,adj=c(0,0.5),cex=fsize[2])
+		}
 	}
 }
 

man/bind.tip.Rd

@@ -9,7 +9,7 @@ bind.tip(tree, tip.label, edge.length=NULL, where=NULL, position=0,
 	\item{tree}{receptor tree.}
 	\item{tip.label}{a string containing the species name for the new tip.}
 	\item{edge.length}{edge length for the new tip (a scalar).}
-	\item{where}{node number to attach new tip. If \code{position>0} then then tip will be attached \emph{below} the specified node. Node numbers can also be tips, in which case the new tip will be added along the terminal edge. To find out the tip number for given species with name \emph{"species"} type: \code{which(tree$tip.label=="species"}.}
+	\item{where}{node number to attach new tip. If \code{position>0} then then tip will be attached \emph{below} the specified node. Node numbers can also be tips, in which case the new tip will be added along the terminal edge. To find out the tip number for given species with name \emph{"species"} type: \code{which(tree$tip.label=="species")}.}
 	\item{position}{distance \emph{below} node to add tip.}
 	\item{interactive}{logical value indicating whether or not the species should be added interactively. (Defaults to \code{FALSE}.)}
 	\item{...}{arguments to be passed to \code{plotTree} (for \code{interactive=TRUE}.)}