Error in draw.clade: invalid subscript type 'list'

[ArtPoon]

Attempting to color branches in very large tree:

> # all sequences
> phy <- read.tree("~/git/flu/data/removeX.ft2.nwk")
> phy <- midpoint(phy)
> phy <- ladderize(phy)
> pal <- gg.rainbow(18)
> # it takes a couple of minutes to generate this layout
> L <- tree.layout(phy)
> res <- 300
> png("~/git/flu/test.png", width=5*res, height=8*res, res=res)
> plot(L, label='n')
> for (i in 1:18) {
+   print(i)
+   # note phy$tip.label == L2$nodes$label[1:Ntip(phy)]
+   idx <- which(grepl(paste("\\(H", i, "[N)]", sep=""), phy$tip.label))
+   draw.clade(L, tips=phy$tip.label[idx], col=pal[i])
+   # label clades using tip farthest from origin
+   #last.tip <- idx[which.max(L2$nodes$r[idx])]
+ }
[1] 1
Error in obj$edges$y0[parents] : invalid subscript type 'list'

[ArtPoon]

Looks like the problem is there:

ggfree/R/tree.R

Lines 1106 to 1109 in a9717ae

	if (obj$layout == 'rectangular') {
	parents <- sapply(e$parent, function(p) which(obj$edges$child==p))
	segments(x0=e$x0, y0=e$y0, y1=obj$edges$y0[parents], col=col, ...)
	}

This returns parents as a list, not an integer vector as expected:

> head(parents)
[[1]]
[1] 4

[[2]]
[1] 5

[[3]]
[1] 6

[[4]]
[1] 7

[[5]]
[1] 8

[[6]]
[1] 9
> table(sapply(parents, length))

    0     1 
    1 45598 
> which.min(sapply(parents, length))
[1] 45519
> parents[45519]
[[1]]
integer(0)
> e[45519,]
      parent child    length isTip x0        x1       y0       y1
86210  67061 84808 0.3695876 FALSE  0 0.3695876 65882.59 65882.59
> which(obj$edges$child == 67061)
integer(0)
> Ntip(phy)
[1] 67060

The node in question is the root.

[ArtPoon]

Potential fix:

@@ -1105,6 +1107,8 @@ draw.clade <- function(obj, tips, col='red', is.mono=TRUE, max.tips=100, ...) {
 
   if (obj$layout == 'rectangular') {
     parents <- sapply(e$parent, function(p) which(obj$edges$child==p))
+    # exclude root node
+    parents <- unlist(parents)
     segments(x0=e$x0, y0=e$y0, y1=obj$edges$y0[parents], col=col, ...)
   }
   else if (obj$layout == 'radial') {

But there are extra lines being drawn: