new option in plotTree.barplot

liamrevell · Oct 18, 2017 · 1007197 · 1007197
1 parent e984799
commit 1007197
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: phytools
-Version: 0.6-30
-Date: 2017-10-03
+Version: 0.6-31
+Date: 2017-10-18
 Title: Phylogenetic Tools for Comparative Biology (and Other Things)
 Author: Liam J. Revell
 Maintainer: Liam J. Revell <liam.revell@umb.edu>
@@ -56,6 +56,6 @@ Description: Package contains various functions for phylogenetic analysis.
 	research.
 License: GPL (>= 2)
 URL: http://github.com/liamrevell/phytools
-Packaged: 2017-10-03 12:00:00 EST
+Packaged: 2017-10-18 12:00:00 EST
 Repository: 
-Date/Publication: 2017-10-03 12:00:00 EST
+Date/Publication: 2017-10-18 12:00:00 EST
diff --git a/R/plotTree.wBars.R b/R/plotTree.wBars.R
@@ -52,7 +52,9 @@ plotTree.boxplot<-function(tree,x,args.plotTree=list(),
 ## written by Liam J. Revell 2016, 2017
 
 plotTree.barplot<-function(tree,x,args.plotTree=list(),
-	args.barplot=list()){
+	args.barplot=list(), ...){
+	if(hasArg(add)) add<-list(...)$add
+	else add<-FALSE
 	cw<-reorder(tree)
 	if(is.data.frame(x)) x<-as.matrix(x)
 	if(is.matrix(x)){
@@ -87,7 +89,7 @@ plotTree.barplot<-function(tree,x,args.plotTree=list(),
 		args.plotTree$mar[3]<-args.barplot$mar[3]
 	if(is.null(args.plotTree$ftype)) args.plotTree$ftype<-"i"
 	if(is.null(args.plotTree$lwd)) args.plotTree$lwd<-1
-	par(mfrow=c(1,2))
+	if(!add) par(mfrow=c(1,2))
 	do.call(plotTree,args.plotTree)
 	par(mar=args.barplot$mar)
 	obj<-do.call(barplot,args.barplot)

diff --git a/man/plotTree.wBars.Rd b/man/plotTree.wBars.Rd
@@ -7,8 +7,8 @@
 plotTree.wBars(tree, x, scale=1, width=NULL, type="phylogram", 
    method="plotTree", tip.labels=FALSE, col="grey", border=NULL, 
    ...)
-plotTree.barplot(tree,x,args.plotTree=list(),args.barplot=list())
-plotTree.boxplot(tree,x,args.plotTree=list(),args.boxplot=list())
+plotTree.barplot(tree, x, args.plotTree=list(), args.barplot=list(), ...)
+plotTree.boxplot(tree, x, args.plotTree=list(), args.boxplot=list())
 }
 \arguments{
  	\item{tree}{an object of class \code{"phylo"}.}
@@ -23,7 +23,7 @@ plotTree.boxplot(tree,x,args.plotTree=list(),args.boxplot=list())
 	\item{args.plotTree}{in \code{plotTree.barplot}, arguments to be passed to \code{\link{plotTree}}.}
 	\item{args.barplot}{in \code{plotTree.barplot}, arguments to be passed to \code{\link{barplot}}.}
 	\item{args.boxplot}{in \code{plotTree.boxplot}, arguments to be passed to \code{\link{boxplot}}.}
-	\item{...}{optional arguments to be passed to \code{\link{plotTree}} or \code{\link{plotSimmap}}.}
+	\item{...}{optional arguments to be passed to \code{\link{plotTree}} or \code{\link{plotSimmap}} in the case of \code{plotTree.wBars}. For \code{plotTree.barplot}, the only optional argument is \code{add}. Generally this should not be used; however it can be used to tell the function to draw the tree & barplot, respectively, in the next two open plotting devices - rather than creating a table of figures in the current plotting device.}
 }
 \description{
 	\code{plotTree.wbars} plots a phylogeny in phylogram or fan style with bars at the tips representing the values for a phenotypic trait.