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

[ArtPoon]

Error in draw.clade: 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: