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Varying border color for plotTree.wBars #56

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Varying border color for plotTree.wBars #56

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a7ffc89
Allow for varying border color
willgearty Oct 30, 2019
1e84b7a
Add documentation
willgearty Oct 30, 2019
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9 changes: 6 additions & 3 deletions R/plotTree.wBars.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
Expand Down Expand Up @@ -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"
Expand All @@ -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))
Expand All @@ -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])
}
}
}
Expand Down
2 changes: 1 addition & 1 deletion man/plotTree.wBars.Rd
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Expand Up @@ -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}}.}
Expand Down