If tree has defined node.labels AddTips() will not change them

[stitam]

Hi,

I'm not sure if I'm using AddTips() incorrectly or there is an issue with the function. Reprex below:

# create a random tree
set.seed(0)
tree <- ape::rtree(10)
# define node labels and plot
tree$node.label <- paste0("Node_", 1:tree$Nnode)
plot(tree, show.node.label = TRUE)

# add a tip
tree2 <- TreeTools::AddTip(tree, where = "t8", label = "new", edgeLength = 0)
# plot, notice that: 1. internal node labels change, 2. "Node_1" is now recycled!
plot(tree2, show.node.label = TRUE)

# Also node.label does not change
tree2$node.label
#> [1] "Node_1" "Node_2" "Node_3" "Node_4" "Node_5" "Node_6" "Node_7" "Node_8"
#> [9] "Node_9"

^{Created on 2024-03-22 with reprex v2.1.0}

This is a problem because tools that make use of the node.label element will produce all sorts of issues downstream.

Not sure this is a proper fix but adding something like this may work:

if ("node.label" %in% names(tree) {
  tree$node.label <- paste0("Node_",  1:tree$Nnode)
}

The names of the internal nodes will still change but the redundancy will be eliminated.

[ms609]

Thanks for the report; AddTip() is not currently set up to support node labels, but I can take a look at this.

[stitam]

To add more context, I was completely unaware of the issue. I built a tree, added the new tips, exported the resulting tree, and then a downstream process produced funky results. It turned out that tree building produced a tree with internal node labels. AddTips() added the tips but did not touch node labels and then ape::write.tree() exported a tree with redundant internal node labels.