object 'last_plot.phylo' not found & Error in seq.default(0, length = n)

[Cactusolo]

Hi,

I have large tree and I plan to use arc.cladelabels function to highlight those bigger clades. My script worked smaller dataset, but when I used for larger dataset. The MAC gives error:
Error in get("last_plot.phylo", envir = .PlotPhyloEnv) :
object 'last_plot.phylo' not found

On Linux machine, it gives error:

Error in seq.default(0, length = n) :
'length.out' must be a non-negative number

Not sure, what's going wrong when scale up.

Thanks!

Miao

> packageVersion("phytools")
[1] ‘0.7.70’

my script:
r```
m(list=ls())
library("phytools")
tree <- read.tree("./husge_phylogeny.tre")
tree2 <- ladderize(tree)
tree2 <- ips::fixNodes(tree2)

plotTree(tree2,type="fan", fsize=0.0002, xlim=c(-6.1,6.1), lwd =0.1)
clade <- unique(sapply(strsplit(tree2$tip.label, "_"), "[", 1)) #clade coded in the tree tips
color = grDevices::colors()[grep('gr(a|e)y', grDevices::colors(), invert = T)]
colx <- sample(color, length(clade))

for(i in 1:length(clade)){
order <- clade[i]
if(length(grep(order, tree2$tip.label))==1){
node <- grep(order, tree2$tip.label)
arc.cladelabels(tree2, order, node=node, orientation="horizontal",ln.offset=1.02,lab.offset=0.9, mark.node=FALSE, cex=0.5)
#print(paste(order, ",", node, sep=""))
}else{
node <- findMRCA(tree2, tree2$tip.label[grep(order, tree2$tip.label)])
#print(paste(order, ",", node, sep=""))
arc.cladelabels(tree2, order, node, lwd=2, ln.offset=1.02, lab.offset=1.05, col=colx[i], cex=0.8)
}
}

[JakoboEU]

I am getting the same error with a tree with 5000+ tips.

plot(cte, type="fan", outline=FALSE, fsize=c(0.01, 1), lwd = c(0.1, 1))
arc.cladelabels(text='Clade', node=19890, ln.offset=1.1, lab.offset=1.16)

The trace looks like

7.| stop("'length.out' must be a non-negative number")
6.| seq.default(0, length = n)
5.| seq(0, length = n)
4.| draw.arc.0(x = 0, y = 0, radius = 124.574682331, angle1 = -Inf, angle2 = Inf, n = 0.05, col = "black", lwd = 1, lend = "round")
3.| do.call("draw.arc.0", c(args[i, ], ...))
2.| draw.arc(x = 0, y = 0, radius = ln.offset * h, deg1 = min(deg), deg2 = max(deg), lwd = lwd, col = col, lend = lend, n = n)
1.| arc.cladelabels(text = "Clade", node = 19890, ln.offset = 1.1, lab.offset = 1.16)

[JakoboEU]

I copy and pasted the function from https://github.com/liamrevell/phytools/blob/6c9f388b9943dac0dc25bba4671bc563361c0e5f/R/utilities.R

The issue appears to be in this piece of code, I am afraid I am not the greatest R coder or debugger. It looks like deg has zero length.

d<-getDescendants(tree,node)
d<-sort(d[d<=Ntip(tree)])
deg<-atan(obj$yy[d]/obj$xx[d])*180/pi
ii<-intersect(which(obj$yy[d]>=0),which(obj$xx[d]<0))
deg[ii]<-180+deg[ii]
ii<-intersect(which(obj$yy[d]<0),which(obj$xx[d]<0))
deg[ii]<-180+deg[ii]
ii<-intersect(which(obj$yy[d]<0),which(obj$xx[d]>=0))
deg[ii]<-360+deg[ii]

draw.arc(x=0,y=0,radius=ln.offset*h,deg1=min(deg),deg2=max(deg),lwd=lwd,col=col,lend=lend,n=n)

Warning in min(deg) : no non-missing arguments to min; returning Inf
Warning in max(deg) : no non-missing arguments to max; returning -Inf
Warning in draw.arc.0(x = 0, y = 0, radius = 124.574682331, angle1 = -Inf,  :
  NAs introduced by coercion to integer range
Error in seq.default(0, length = n) : 
  'length.out' must be a non-negative number

[JakoboEU]

Managed to fix these with two changes.

1. Make sure the tree is passed as an argument to arc.cladelabels
2. Need to handle deg containing nulls. Therefore the calls to min, max, median, and range inside arc.cladelabels all need the na.rm = T argument.

Modified function to be:

library(plotrix)
arc.cladelabels.fixed <- function(tree=NULL,text,node=NULL,ln.offset=1.02,
	lab.offset=1.06,cex=1,orientation="curved",...){
	obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
	if(obj$type!="fan") stop("method works only for type=\"fan\"")
	h<-max(sqrt(obj$xx^2+obj$yy^2))
	if(hasArg(mark.node)) mark.node<-list(...)$mark.node
	else mark.node<-TRUE
	if(hasArg(interactive)) interactive<-list(...)$interactive
	else {
		if(is.null(node)) interactive<-TRUE
		else interactive<-FALSE
	}
	if(interactive) node<-getnode()
	if(hasArg(lwd)) lwd<-list(...)$lwd
	else lwd<-par()$lwd
	if(hasArg(col)) col<-list(...)$col
	else col<-par()$col
	if(hasArg(lend)) lend<-list(...)$lend
	else lend<-par()$lend
	if(hasArg(clockwise)) clockwise<-list(...)$clockwise
	else clockwise<-TRUE
	if(hasArg(n)) n<-list(...)$n
	else n<-0.05
	if(mark.node) points(obj$xx[node],obj$yy[node],pch=21,
		bg="red")
	if(is.null(tree)){
		tree<-list(edge=obj$edge,tip.label=1:obj$Ntip,
			Nnode=obj$Nnode)
		class(tree)<-"phylo"
	}
	d<-getDescendants(tree,node)
	d<-sort(d[d<=Ntip(tree)])
	
	deg<-atan(obj$yy[d]/obj$xx[d])*180/pi
	
	ii<-intersect(which(obj$yy[d]>=0),which(obj$xx[d]<0))
	deg[ii]<-180+deg[ii]
	
	ii<-intersect(which(obj$yy[d]<0),which(obj$xx[d]<0))
	deg[ii]<-180+deg[ii]
	
	ii<-intersect(which(obj$yy[d]<0),which(obj$xx[d]>=0))
	deg[ii]<-360+deg[ii]
	
	deg1 <- min(deg, na.rm = T)
	deg2 <- max(deg, na.rm = T)
	draw.arc(x=0,y=0,radius=ln.offset*h,deg1=deg1, deg2=deg2,lwd=lwd,col=col,lend=lend,n=n)
	
	if(orientation=="curved")
		arctext(text, radius=lab.offset*h, middle=mean(range(deg * pi/180, na.rm = T)), cex=cex, clockwise=clockwise)
	else if(orientation=="horizontal") {
	  deg_med <- median(deg, na.rm = T)
		x0<-lab.offset * cos(deg_med*pi/180)*h
		y0<-lab.offset * sin(deg_med*pi/180)*h
		text(x=x0,y=y0,label=text,
		adj=c(if(x0>=0) 0 else 1,if(y0>=0) 0 else 1),
		offset=0,cex=cex)
	}
}

Then call this as:

plot(cte, type="fan", outline=FALSE, fsize=c(0.01, 1), lwd = c(0.1, 1))
arc.cladelabels.fixed(text = 'family', node = 19890, ln.offset=1.1, lab.offset=1.16, tree = tree, orientation="curved")