1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
|
## 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, 2018, 2020, 2023
collapseTree<-function(tree,...){
if(!inherits(tree,"phylo")) stop("tree should be an object of class \"phylo\".")
if(inherits(tree,"simmap")) tree<-as.phylo(tree)
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(...)$drop.extinct
else drop.extinct<-TRUE
if(hasArg(sleep)) sleep<-list(...)$sleep
else sleep<-0.05
if(is.null(tree$edge.length)){
no.edge<-TRUE
tree<-compute.brlen(tree,power=0.5)
} else no.edge<-FALSE
cat("Click on the nodes that you would like to collapse...\n")
flush.console()
## turn off locator bell (it's annoying)
options(locatorBell=FALSE)
## check for node labels
if(is.null(tree$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)
rect(par()$usr[1],par()$usr[4]-3*strheight("W"),par()$usr[2],par()$usr[4],
border=0,col=make.transparent("blue",0.2))
textbox(x=par()$usr[1:2],y=par()$usr[4],
c("Click nodes to collapse or expand\nRIGHT CLICK (or FINISH in RStudio) to stop"),
justify="c",border=0)
dev.flush()
x<-unlist(locator(1))
if(!is.null(x)){
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(!is.null(x)){
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],...)
rect(par()$usr[1],par()$usr[4]-3*strheight("W"),
par()$usr[2],par()$usr[4],
border=0,col=make.transparent("blue",0.2))
textbox(x=par()$usr[1:2],y=par()$usr[4],
c("Click nodes to collapse or expand\nRIGHT CLICK (or FINISH in RStudio) to stop"),
justify="c",border=0)
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)
}
Sys.sleep(sleep)
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$y.lim,
tips=M[i,],maxY=NULL,...)
rect(par()$usr[1],par()$usr[4]-3*strheight("W"),
par()$usr[2],par()$usr[4],
border=0,col=make.transparent("blue",0.2))
textbox(x=par()$usr[1:2],y=par()$usr[4],
c("Click nodes to collapse or expand\nRIGHT CLICK (or FINISH in RStudio) to stop"),
justify="c",border=0)
if(nodes||i==nrow(M)){
lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
points(x=lastPP$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$Nnode+Ntip(tree)],pch=21,
col="blue",bg="white",cex=1.2)
}
Sys.sleep(sleep)
dev.flush()
}
}
} else {
cat("Collapsing to the root is not permitted. Choose another node.\n")
flush.console()
}
x<-unlist(locator(1))
if(!is.null(x)){
y<-x[2]
x<-x[1]
lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
d<-sqrt((x-lastPP$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)
}
|
