From a7ffc89c36f471497b10d731d48d0dc3f5f91c8b Mon Sep 17 00:00:00 2001
From: Will Gearty <willgearty@gmail.com>
Date: Wed, 30 Oct 2019 14:39:12 -0500
Subject: [PATCH 1/2] Allow for varying border color

---
 R/plotTree.wBars.R | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/R/plotTree.wBars.R b/R/plotTree.wBars.R
index 0b2ebada..2ee3bcdb 100644
--- a/R/plotTree.wBars.R
+++ b/R/plotTree.wBars.R
@@ -108,7 +108,7 @@ plotTree.barplot<-function(tree,x,args.plotTree=list(),
 ## written by Liam J. Revell 2014, 2015, 2018, 2019
 
 plotTree.wBars<-function(tree,x,scale=NULL,width=NULL,type="phylogram",
-	method="plotTree",tip.labels=FALSE,col="grey",border=NULL,...){
+	method="plotTree",tip.labels=FALSE,col="grey",border="black",...){
 	if(!inherits(tree,"phylo")) stop("tree should be an object of class \"phylo\".")
 	if(is.null(scale)){ 
 		scale<-0.3*max(nodeHeights(tree))/diff(range(x))
@@ -201,6 +201,9 @@ plotTree.wBars<-function(tree,x,scale=NULL,width=NULL,type="phylogram",
 		if(length(col)<Ntip(tree)) col<-rep(col,ceiling(Ntip(tree)/length(col)))[1:Ntip(tree)]
 		if(is.null(names(col))) names(col)<-tree$tip.label
 		col<-col[tree$tip.label]
+		if(length(border)<Ntip(tree)) border<-rep(border,ceiling(Ntip(tree)/length(border)))[1:Ntip(tree)]
+		if(is.null(names(border))) names(border)<-tree$tip.label
+		border<-border[tree$tip.label]
 		if(type=="phylogram"){
 			if(hasArg(direction)) direction<-list(...)$direction
 			else direction<-"rightwards"
@@ -213,7 +216,7 @@ plotTree.wBars<-function(tree,x,scale=NULL,width=NULL,type="phylogram",
 				y1<-y4<-dy-w/2
 				y2<-y3<-dy+w/2
 				polygon(c(x1,x2,x3,x4)-min(0,min(x)),
-					c(y1,y2,y3,y4),col=col[i],border=border)
+					c(y1,y2,y3,y4),col=col[i],border=border[i])
 			}
 		} else if(type=="fan"){
 			h<-max(nodeHeights(tree))
@@ -232,7 +235,7 @@ plotTree.wBars<-function(tree,x,scale=NULL,width=NULL,type="phylogram",
 				x4<-s*x[i]*cos(theta)+x1
 				y4<-s*x[i]*sin(theta)+y1
 				polygon(c(x1,x2,x3,x4),c(y1,y2,y3,y4),col=col[i],
-					border=border)
+					border=border[i])
 			}	
 		}
 	}

From 1e84b7a5e2178ea0111472f96cf27deece399b17 Mon Sep 17 00:00:00 2001
From: Will Gearty <willgearty@gmail.com>
Date: Wed, 30 Oct 2019 14:42:01 -0500
Subject: [PATCH 2/2] Add documentation

---
 man/plotTree.wBars.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/plotTree.wBars.Rd b/man/plotTree.wBars.Rd
index 0360887f..f4770dde 100644
--- a/man/plotTree.wBars.Rd
+++ b/man/plotTree.wBars.Rd
@@ -19,7 +19,7 @@ plotTree.boxplot(tree, x, args.plotTree=list(), args.boxplot=list())
 	\item{method}{plotting method to use. Can be \code{"plotTree"} (for \code{\link{plotTree}}) or \code{"plotSimmap"} (for \code{\link{plotSimmap}}).}
 	\item{tip.labels}{argument indicating whether or not tip labels should be plotted. Defaults to \code{tip.labels=FALSE}.}
 	\item{col}{colors of the plotted bars. Can be a single value or a vector with length equal to the number of tips in the tree.}
-	\item{border}{single value specifying the color of the border for the plotted bars. Defaults to \code{border=NULL}, which means that black borders will be plotted.}
+	\item{border}{colors of the borders of the plotted bars. Can be a single value or a vector with length equal to the number of tips in the tree.}
 	\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}}.}