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## function to plot a tree with dots/circles for a plotted phenotype
## written by Liam J. Revell 2016, 2017, 2018, 2023
dotTree<-function(tree,x,legend=TRUE,method="plotTree",standardize=FALSE,...){
if(is.data.frame(x)) x<-as.matrix(x)
if(hasArg(data.type)) data.type<-list(...)$data.type
else {
## try to detect type
if(is.numeric(x)) data.type<-"continuous"
else data.type<-"discrete"
}
if(data.type=="continuous"){
if(hasArg(colors)) colors<-list(...)$colors
else colors<-"blue"
dotTree.continuous(tree,x,colors[1],legend,method,standardize,...)
} else if(data.type=="discrete"){
if(hasArg(colors)) colors<-list(...)$colors
else {
ss<-unique(as.vector(x))
colors<-setNames(palette()[1:length(ss)],ss)
}
dotTree.discrete(tree,x,colors,legend,method,...)
}
}
dotTree.continuous<-function(tree,x,color,legend,method,standardize,...){
if(hasArg(border)) border<-list(...)$border
else border<-par()$fg
if(hasArg(cex.dot)) cex.dot<-list(...)$cex.dot
else cex.dot<-1.0
if(is.data.frame(x)) x<-as.matrix(x)
if(is.matrix(x)&&method=="plotTree"){
if(ncol(x)>1) method<-"phylogram"
else x<-x[,1]
}
if(hasArg(fsize)) fsize<-list(...)$fsize
else fsize<-c(1,0.8)
if(length(fsize)==1) fsize<-rep(fsize,2)
if(hasArg(x.space)) x.space<-list(...)$x.space
else x.space<-0.1
if(hasArg(k)) k<-list(...)$k
else k<-0.8
## reorder tree
tree<-reorder(tree,"cladewise")
## if standardize==TRUE
if(standardize){
if(is.matrix(x)){
sd<-apply(x,2,function(x) sqrt(var(x)))
x<-(x-matrix(rep(1,Ntip(tree)),Ntip(tree),1)%*%colMeans(x))/
(matrix(rep(1,Ntip(tree)),Ntip(tree),1)%*%sd)
} else if(is.vector(x)) x<-(x-mean(x))/sqrt(var(x))
}
## in case any x<0
min.x<-min(x)
max.x<-max(x)
if(any(x<0)) x<-x-min(x)
if(method=="plotTree"){
fsize<-fsize[1]
x<-x[tree$tip.label]
## plot tree
plotTree(tree,offset=1.7,ylim=c(-Ntip(tree)/25,
Ntip(tree)),...)
## get last phylo plot parameters
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
x.tip<-obj$xx[1:obj$Ntip]
y.tip<-obj$yy[1:obj$Ntip]
## plot points
rr<-(k*x/max(x)+x.space)/2*diff(par()$usr[1:2])/
diff(par()$usr[3:4])
if(k<=0.8&&any(rr>(strwidth("W")*fsize/2)))
rr<-rr/max(rr)*strwidth("W")*fsize/2
nulo<-mapply(draw.circle,x=x.tip+1.2*strwidth("W"),y=y.tip,
radius=cex.dot*rr,MoreArgs=list(nv=200,col=color,border=border))
## add legend
if(legend){
h<-dot.legend(x=par()$usr[1]+0.1*max(nodeHeights(tree)),
y=0,min.x,max.x,Ntip=Ntip(tree),
method="plotTree",...)
if(standardize) text(h,0.1*(1+par()$usr[3]),"(SD units)",pos=4)
}
} 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(...)$ylim
else ylim<-c(if(legend) -0.1 else 0,if(labels) 1.1 else 1)
## plot tree
plot.new()
par(mar=mar)
plot.window(xlim=xlim,ylim=ylim)
h<-phylogram(tree,...)
## get last phylo plot parameters
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
x.tip<-rep(h,obj$Ntip)
y.tip<-obj$yy[1:obj$Ntip]
## 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[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=cex.dot*rr[,i],MoreArgs=list(nv=200,col=color,
border=border))
}
## 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])
}
}
}
dotTree.discrete<-function(tree,x,color,legend,method,...){
if(hasArg(border)) border<-list(...)$border
else border<-par()$fg
if(hasArg(cex.dot)) cex.dot<-list(...)$cex.dot
else cex.dot<-1.0
if(is.data.frame(x)) x<-as.matrix(x)
if(is.matrix(x)&&method=="plotTree"){
if(ncol(x)>1) method<-"phylogram"
else x<-x[,1]
}
if(hasArg(fsize)) fsize<-list(...)$fsize
else fsize<-c(1,0.8)
if(length(fsize)==1) fsize<-rep(fsize,2)
if(hasArg(x.space)) x.space<-list(...)$x.space
else x.space<-0.1
## reorder tree
tree<-reorder(tree,"cladewise")
if(method=="plotTree"){
x<-x[tree$tip.label]
## plot tree
plotTree(tree,offset=1.7,ylim=c(-1/25*Ntip(tree),
Ntip(tree)),...)
## get last phylo plot parameters
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
x.tip<-obj$xx[1:obj$Ntip]
y.tip<-obj$yy[1:obj$Ntip]
## plot points
r<-min(0.8/2*diff(par()$usr[1:2])/diff(par()$usr[3:4]),
strwidth("W")*fsize/2)
nulo<-mapply(draw.circle,x=x.tip+1.2*strwidth("W"),y=y.tip,
col=color[as.character(x)],MoreArgs=list(nv=200,
radius=cex.dot*r,border=border))
if(legend){
add.simmap.legend(colors=color,prompt=FALSE,
vertical=FALSE,shape="circle",
x=par()$usr[1]+0.1*max(nodeHeights(tree)),
y=-1/25*Ntip(tree),border=border)
}
} else if(method=="phylogram"){
if(is.vector(x)) x<-as.matrix(x)
x[]<-x[tree$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=mar)
plot.window(xlim=xlim,ylim=ylim)
h<-phylogram(tree,...)
## get last phylo plot parameters
obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
x.tip<-rep(h,obj$Ntip)
y.tip<-obj$yy[1:obj$Ntip]
## plot points
r<-min(0.8/2*diff(par()$usr[1:2])/diff(par()$usr[3:4])/(Ntip(tree)-1),
strwidth("W")*fsize/2)
for(i in 1:ncol(x)){
nulo<-mapply(draw.circle,x=x.tip+1.2*strwidth("W")+x.space*(i-1),
y=y.tip,col=color[as.character(x[,i])],MoreArgs=list(nv=20,
radius=cex.dot*r,border=border))
}
## add legend
if(legend){
add.simmap.legend(colors=color,prompt=FALSE,
vertical=FALSE,shape="circle",x=-0.45,y=-0.06,
border=border)
}
if(labels){
text(x=seq(max(x.tip)+1.2*strwidth("W"),
max(x.tip)+1.2*strwidth("W")+x.space*(ncol(x)-1),by=x.space),
y=rep(1.02,ncol(x)),colnames(x),srt=70,adj=c(0,0.5),cex=fsize[2])
}
}
}
## dot legend
## written by Liam J. Revell 2016, 2023
dot.legend<-function(x,y,min,max,Ntip,length=5,prompt=FALSE,
method="plotTree",...){
if(hasArg(border)) border<-list(...)$border
else border<-par()$fg
if(hasArg(cex.dot)) cex.dot<-list(...)$cex.dot
else cex.dot<-1.0
if(hasArg(cex)) cex<-list(...)$cex
else cex<-1
if(hasArg(fsize)) fsize<-list(...)$fsize
else fsize<-1
if(hasArg(colors)) colors<-list(...)$colors
else colors<-"blue"
if(hasArg(leg.space)) leg.space<-list(...)$leg.space
else leg.space<-0.2
if(hasArg(k)) k<-list(...)$k
else k<-0.8
if(prompt){
obj<-locator(1)
x<-obj$x
y<-obj$y
}
if(method=="plotTree"){
text(x,y-0.5*(Ntip/25),round(min,2),pos=1,cex=cex)
s<-(k*max(min,0)/min(max,max+min)+0.1)/2*diff(par()$usr[1:2])/
diff(par()$usr[3:4])
e<-(k+0.1)/2*diff(par()$usr[1:2])/diff(par()$usr[3:4])
rr<-seq(s,e,length.out=length)
if(k<=0.8&&any(rr>(strwidth("W")*fsize/2)))
rr<-rr/max(rr)*strwidth("W")*fsize/2
temp<-c(0,cumsum((1+leg.space)*rep(2*max(rr),length-1)))
nulo<-mapply(draw.circle,x=x+temp,y=rep(y,length),radius=cex.dot*rr,
MoreArgs=list(nv=200,col=colors,border=border))
text(max(x+temp),y-0.5*(Ntip/25),round(max,2),pos=1,cex=cex)
y1<-0.1/25*Ntip
lines(c(x,max(x+temp)),rep(y-0.5*(Ntip/25)-y1,2))
lines(c(x,x),y-c(y1+0.5*(Ntip/25),2*y1+0.5*(Ntip/25)))
lines(c(max(x+temp),max(x+temp)),y-c(y1+0.5*(Ntip/25),2*y1+0.5*(Ntip/25)))
} else if(method=="phylogram"){
text(x,y-0.04,round(min,2),pos=1,cex=cex)
s<-(k*max(min,0)/(min(max,max+min))+0.1)/2*
diff(par()$usr[1:2])/diff(par()$usr[3:4])/(Ntip-1)
e<-(k+0.1)/2*diff(par()$usr[1:2])/diff(par()$usr[3:4])/(Ntip-1)
rr<-seq(s,e,length.out=length)
if(k<=0.8&&any(rr>(strwidth("W")*fsize/2)))
rr<-rr/max(rr)*strwidth("W")*fsize/2
temp<-c(0,cumsum((1+leg.space)*rep(2*max(rr),length-1)))
nulo<-mapply(draw.circle,x=x+temp,y=rep(y,length),radius=cex.dot*rr,
MoreArgs=list(nv=200,col=colors,border=border))
text(max(x+temp),y-0.04,round(max,2),pos=1,cex=cex)
y1<-0.01
lines(c(x,max(x+temp)),rep(y-0.02-y1,2))
lines(c(x,x),y-c(y1+0.02,2*y1+0.02))
lines(c(max(x+temp),max(x+temp)),y-c(y1+0.02,2*y1+0.02))
}
invisible(max(x+temp)+0.5*max(rr))
}
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