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collapseTree.R
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collapseTree.R
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## function to interactively expand and contract subtrees on a phylogeny
## inspired by the phylogeny interface of sharksrays.org by Gavin Naylor
## written by Liam J. Revell 2015, 2016, 2017
collapseTree<-function(tree,...){
if(!inherits(tree,"phylo")) stop("tree should be an object of class \"phylo\".")
if(hasArg(nodes)) nodes<-list(...)$nodes
else nodes<-TRUE
if(hasArg(hold)) hold<-list(...)$hold
else hold<-TRUE
if(hasArg(drop.extinct)) drop.extinct<-list(...)$drop.extinct
else drop.extinct=FALSE
if(is.null(tree$edge.length)){
no.edge<-TRUE
tree<-compute.brlen(tree,power=0.5)
} else no.edge<-FALSE
cat("Click on the nodes that you would like to collapse...\n")
## turn off locator bell (it's annoying)
options(locatorBell=FALSE)
## check for node labels
if(is.null(tree$node.label)) tree$node.label<-as.character(Ntip(tree)+1:tree$Nnode)
else if(any(tree$node.label=="")){
tree$node.label[which(tree$node.label)==""]<-
which(tree$node.label=="")+Ntip(tree)
}
## remove any spaces
tree$node.label<-sapply(tree$node.label,gsub,pattern=" ",replacement="_")
tree$tip.label<-sapply(tree$tip.label,gsub,pattern=" ",replacement="_")
## copy original tree:
otree<-tree<-reorder(tree)
## plot initial tree:
if(hold) dev.hold()
fan(tree,...)
lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
points(x=lastPP$xx[1:Ntip(tree)],y=lastPP$yy[1:Ntip(tree)],
pch=21,col="blue",bg="white",cex=0.8)
points(x=lastPP$xx[1:tree$Nnode+Ntip(tree)],
y=lastPP$yy[1:tree$Nnode+Ntip(tree)],pch=21,
col="blue",bg="white",cex=1.2)
check<-textbox(x=c(par()$usr[1],par()$usr[1]+
0.1*(par()$usr[2]-par()$usr[1])),
y=par()$usr[4],c("click to stop"),justify="c")
dev.flush()
x<-unlist(locator(1))
y<-x[2]
x<-x[1]
d<-sqrt((x-lastPP$xx)^2+(y-lastPP$yy)^2)
nn<-which(d==min(d,na.rm=TRUE))
## collapse tree & replot:
while(!(x>par()$usr[1]&&x<par()$usr[1]+0.1*(par()$usr[2]-par()$usr[1])&&
y>check&&y<par()$usr[4])){
obj<-list(tree)
if(nn>(Ntip(tree)+1)){
obj<-splitTree(tree,list(node=nn,
bp=tree$edge.length[which(tree$edge[,2]==nn)]))
obj[[1]]$tip.label[which(obj[[1]]$tip.label=="NA")]<-
tree$node.label[nn-Ntip(tree)]
tips<-which(tree$tip.label%in%obj[[1]]$tip.label)
theta<-atan(lastPP$yy[nn]/lastPP$xx[nn])
if(lastPP$yy[nn]>0&&lastPP$xx[nn]<0) theta<-pi+theta
else if(lastPP$yy[nn]<0&&lastPP$xx[nn]<0) theta<-pi+theta
else if(lastPP$yy[nn]<0&&lastPP$xx[nn]>0) theta<-2*pi+theta
ii<-which((c(tips,Ntip(tree)+1)-c(0,tips))>1)
if(ii>1&&ii<=length(tips))
tips<-c(tips[1:(ii-1)],theta/(2*pi)*Ntip(tree),tips[ii:length(tips)])
else if(ii==1) tips<-c(theta/(2*pi)*Ntip(tree),tips)
else if(ii>length(tips)) tips<-c(tips,theta/(2*pi)*Ntip(tree))
tree<-read.tree(text=write.tree(obj[[1]]))
M<-matrix(NA,min(c(max(4,Ntip(obj[[2]])),10)),length(tips))
for(i in 1:ncol(M)) M[,i]<-seq(from=tips[i],to=i,length.out=nrow(M))
colnames(M)<-tree$tip.label
maxY<-seq(from=sum(sapply(obj,Ntip))-length(obj)+1,to=Ntip(tree),length.out=nrow(M))
pw<-reorder(tree,"pruningwise")
H<-nodeHeights(tree)
for(i in 1:nrow(M)){
if(hold) dev.hold()
fan(tree,pw,H,xlim=lastPP$x.lim,ylim=lastPP$y.lim,
tips=M[i,],maxY=maxY[i],...)
if(nodes||i==nrow(M)){
lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
points(x=lastPP$xx[1:Ntip(tree)],y=lastPP$yy[1:Ntip(tree)],
pch=21,col="blue",bg="white",cex=0.8)
points(x=lastPP$xx[1:tree$Nnode+Ntip(tree)],
y=lastPP$yy[1:tree$Nnode+Ntip(tree)],pch=21,
col="blue",bg="white",cex=1.2)
}
dev.flush()
}
} else if(nn<=Ntip(tree)) {
if(tree$tip.label[nn]%in%otree$node.label){
on<-which(otree$node.label==tree$tip.label[nn])+Ntip(otree)
obj<-splitTree(otree,list(node=on,
bp=otree$edge.length[which(otree$edge[,2]==on)]))
nlabel<-tree$tip.label[nn]
tree$tip.label[nn]<-"NA"
if(nn==1) tips<-c(rep(nn,Ntip(obj[[2]])),(nn+1):Ntip(tree))
else if(nn>1&&nn<Ntip(tree)) tips<-c(1:(nn-1),rep(nn,Ntip(obj[[2]])),(nn+1):Ntip(tree))
else if(nn==Ntip(tree)) tips<-c(1:(nn-1),rep(nn,Ntip(obj[[2]])))
tree<-read.tree(text=write.tree(paste.tree(tree,obj[[2]])))
M<-matrix(NA,min(c(max(4,Ntip(obj[[2]])),10)),length(tips))
for(i in 1:ncol(M)) M[,i]<-seq(from=tips[i],to=i,length.out=nrow(M))
colnames(M)<-tree$tip.label
pw<-reorder(tree,"pruningwise")
H<-nodeHeights(tree)
for(i in 1:nrow(M)){
if(hold) dev.hold()
fan(tree,pw,H,xlim=lastPP$x.lim,ylim=lastPP$y.lim,
tips=M[i,],maxY=NULL,...)
if(nodes||i==nrow(M)){
lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
points(x=lastPP$xx[1:Ntip(tree)],y=lastPP$yy[1:Ntip(tree)],
pch=21,col="blue",bg="white",cex=0.8)
points(x=lastPP$xx[1:tree$Nnode+Ntip(tree)],
y=lastPP$yy[1:tree$Nnode+Ntip(tree)],pch=21,
col="blue",bg="white",cex=1.2)
}
dev.flush()
}
}
} else {
cat("Collapsing to the root is not permitted. Choose another node.\n")
flush.console()
}
check<-textbox(x=c(par()$usr[1],par()$usr[1]+
0.1*(par()$usr[2]-par()$usr[1])),y=par()$usr[4],
c("click to stop"),justify="c")
x<-unlist(locator(1))
y<-x[2]
x<-x[1]
lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
d<-sqrt((x-lastPP$xx)^2+(y-lastPP$yy)^2)
nn<-which(d==min(d,na.rm=TRUE))
}
## turn locator bell back on
options(locatorBell=TRUE)
if(drop.extinct){
if(!is.ultrametric(otree))
cat("Input tree was not ultrametric. Ignoring argument drop.extinct.\n")
else {
th<-setNames(sapply(1:Ntip(tree),nodeheight,tree=tree),tree$tip.label)
tips<-names(th)[which(th<(mean(sapply(1:Ntip(otree),
nodeheight,tree=otree))-.Machine$double.eps^0.5))]
tree<-drop.tip(tree,tips)
}
}
if(no.edge) tree$edge.length<-NULL
tree
}
circles<-function(x,y,r,col="blue")
nulo<-mapply(draw.circle,x=x,y=y,radius=r,MoreArgs=list(border=col,
col="white",nv=20))
# simplified function to plot tree in type "fan"
# written by Liam J. Revell 2015
fan<-function(tree,pw=NULL,nH=NULL,colors="black",fsize=0.6,ftype="i",lwd=1,mar=rep(0.1,4),
add=FALSE,part=1,xlim=NULL,ylim=NULL,tips=NULL,maxY=NULL,...){
## set colors
if(length(colors)==1) colors<-rep(colors,nrow(tree$edge))
## set font
ftype<-which(c("off","reg","b","i","bi")==ftype)-1
# reorder
cw<-tree
if(is.null(pw)) pw<-reorder(tree,"pruningwise")
# count nodes and tips
n<-Ntip(cw)
m<-cw$Nnode
# get Y coordinates on uncurved space
Y<-vector(length=m+n)
if(is.null(tips)) tips<-1:n
if(part<1.0) Y[cw$edge[cw$edge[,2]<=n,2]]<-0:(n-1)
else Y[cw$edge[cw$edge[,2]<=n,2]]<-tips
nodes<-unique(pw$edge[,1])
for(i in 1:m){
desc<-pw$edge[which(pw$edge[,1]==nodes[i]),2]
Y[nodes[i]]<-(min(Y[desc])+max(Y[desc]))/2
}
if(is.null(maxY)) maxY<-max(Y)
Y<-setNames(Y/maxY*2*pi,1:(n+m))
Y<-part*cbind(Y[as.character(tree$edge[,2])],Y[as.character(tree$edge[,2])])
R<-if(is.null(nH)) nodeHeights(cw) else nH
# now put into a circular coordinate system
x<-R*cos(Y)
y<-R*sin(Y)
# optimize x & y limits
par(mar=mar)
offsetFudge<-1.37 # empirically determined
offset<-0
if(is.null(xlim)||is.null(ylim)){
pp<-par("pin")[1]
sw<-fsize*(max(strwidth(cw$tip.label,units="inches")))+
offsetFudge*offset*fsize*strwidth("W",units="inches")
alp<-optimize(function(a,H,sw,pp) (2*a*1.04*max(H)+2*sw-pp)^2,H=R,sw=sw,pp=pp,
interval=c(0,1e6))$minimum
if(part<=0.25) x.lim<-y.lim<-c(0,max(R)+sw/alp)
else if(part>0.25&&part<=0.5){
x.lim<-c(-max(R)-sw/alp,max(R)+sw/alp)
y.lim<-c(0,max(R)+sw/alp)
} else x.lim<-y.lim<-c(-max(R)-sw/alp,max(R)+sw/alp)
xlim<-x.lim
ylim<-y.lim
}
# plot tree
if(!add) plot.new()
plot.window(xlim=xlim,ylim=ylim,asp=1)
# plot radial lines (edges)
segments(x[,1],y[,1],x[,2],y[,2],col=colors,lwd=lwd,lend=2)
# plot circular lines
ii<-sapply(1:m+n,function(x,y) which(y==x),y=cw$edge)
r<-sapply(1:m+n,function(x,y,R) R[match(x,y)],y=cw$edge,R=R)
a1<-sapply(ii,function(x,Y) min(Y[x]),Y=Y)
a2<-sapply(ii,function(x,Y) max(Y[x]),Y=Y)
draw.arc(rep(0,tree$Nnode),rep(0,tree$Nnode),r,a1,a2,lwd=lwd,col=colors)
# plot labels
cw$tip.label<-gsub("_"," ",cw$tip.label)
for(i in 1:n){
ii<-which(cw$edge[,2]==i)
aa<-Y[ii,2]/(2*pi)*360
adj<-if(aa>90&&aa<270) c(1,0.25) else c(0,0.25)
tt<-if(aa>90&&aa<270) paste(cw$tip.label[i]," ",sep="") else paste(" ",
cw$tip.label[i],sep="")
aa<-if(aa>90&&aa<270) 180+aa else aa
if(ftype) text(x[ii,2],y[ii,2],tt,srt=aa,adj=adj,cex=fsize,font=ftype)
}
PP<-list(type="fan",use.edge.length=TRUE,node.pos=1,
show.tip.label=if(ftype) TRUE else FALSE,show.node.label=FALSE,
font=ftype,cex=fsize,adj=0,srt=0,no.margin=FALSE,label.offset=offset,
x.lim=xlim,y.lim=ylim,direction="rightwards",tip.color="black",
Ntip=Ntip(cw),Nnode=cw$Nnode,edge=cw$edge,
xx=c(x[sapply(1:n,function(x,y) which(x==y)[1],y=tree$edge[,2]),2],x[1,1],
if(m>1) x[sapply(2:m+n,function(x,y) which(x==y)[1],y=tree$edge[,2]),2] else c()),
yy=c(y[sapply(1:n,function(x,y) which(x==y)[1],y=tree$edge[,2]),2],y[1,1],
if(m>1) y[sapply(2:m+n,function(x,y) which(x==y)[1],y=tree$edge[,2]),2] else c()))
assign("last_plot.phylo",PP,envir=.PlotPhyloEnv)
}