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Custom expansion constant and x/y adjustments for cladelabels #55

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Custom expansion constant and x/y adjustments for cladelabels #55

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504fe13
Custom expansion constant and x/y adjustments
willgearty Oct 30, 2019
c10a8b1
Avoid existing function name
willgearty Oct 30, 2019
6fdce1a
Add documentation
willgearty Oct 30, 2019
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10 changes: 5 additions & 5 deletions R/utilities.R
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Original file line number Diff line number Diff line change
Expand Up @@ -856,7 +856,7 @@ markChanges<-function(tree,colors=NULL,cex=1,lwd=2,plot=TRUE){
## function to label clades
## written by Liam J. Revell 2014, 2015
cladelabels<-function(tree=NULL,text,node,offset=NULL,wing.length=NULL,cex=1,
orientation="vertical"){
orientation="vertical",move=c(0,0),exp.c=0.7){
lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
if(is.null(tree)){
wing.length<-1
Expand All @@ -871,17 +871,17 @@ cladelabels<-function(tree=NULL,text,node,offset=NULL,wing.length=NULL,cex=1,
if(is.null(offset)) offset<-0.5
xx<-mapply(labelSubTree,node,text,
MoreArgs=list(tree=tree,pp=lastPP,offset=offset,wl=wing.length,cex=cex,
orientation=orientation))
orientation=orientation,move=move,exp.c=exp.c))
}

## internal function used by cladelabels
## written by Liam J. Revell 2014, 2015
labelSubTree<-function(tree,nn,label,pp,offset,wl,cex,orientation){
labelSubTree<-function(tree,nn,label,pp,offset,wl,cex,orientation,move,exp.c){
if(is.null(wl)) wl<-1
tree<-reorder(tree)
tips<-getDescendants(tree,nn)
tips<-tips[tips<=Ntip(tree)]
ec<-0.7 ## expansion constant
ec<-exp.c ## expansion constant
sw<-pp$cex*max(strwidth(tree$tip.label[tips]))
sh<-pp$cex*max(strheight(tree$tip.label))
cw<-mean(strwidth(LETTERS)*cex)
Expand All @@ -894,7 +894,7 @@ labelSubTree<-function(tree,nn,label,pp,offset,wl,cex,orientation){
c(y[1]-ec*sh,y[1]-ec*sh))
lines(c(h-wl*cw,h),
c(y[2]+ec*sh,y[2]+ec*sh))
text(h+cw,mean(y),
text(h+cw+move[1],mean(y)+move[2],
label,srt=if(orientation=="horizontal") 0 else 90,
adj=if(orientation=="horizontal") 0 else 0.5,cex=cex)
}
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4 changes: 3 additions & 1 deletion man/cladelabels.Rd
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Expand Up @@ -4,7 +4,7 @@
\title{Add labels to subtrees of a plotted phylogeny}
\usage{
cladelabels(tree=NULL, text, node, offset=NULL, wing.length=NULL, cex=1,
orientation="vertical")
orientation="vertical",move=c(0,0),exp.c=0.7)
arc.cladelabels(tree=NULL, text, node=NULL, ln.offset=1.02,
lab.offset=1.06, cex=1, orientation="curved",...)
}
Expand All @@ -16,6 +16,8 @@ arc.cladelabels(tree=NULL, text, node=NULL, ln.offset=1.02,
\item{wing.length}{length of the wings to add to the top & bottom of the label bar (in character widths).}
\item{cex}{character expansion factor.}
\item{orientation}{orientation of the text. Can be \code{orientation = "vertical"} (the default) or \code{"horizontal"}.}
\item{move}{horizontal and vertical adjustments}
\item{exp.c}{expansion constant}
\item{ln.offset}{line offset (as a function of total tree height) for \code{arc.cladelabels}.}
\item{lab.offset}{label offset for \code{arc.cladelabels}.}
\item{...}{optional arguments for \code{arc.cladelabels}.}
Expand Down