contMap crashes if ancestral states are named with node names

[bredelings]

Hi Liam! I hope you are enjoying the holidays.

I wrote a short script to visualize GC content on a tree. I need to use external sequence reconstructions, and I have:

• a newick file with names like A30 on the internal nodes
• a FASTA file with sequences for the internal nodes.

It looks like contMap( ) crashes if anc.states contains node names:

> contMap(tree, gc_values[tree$tip.label],method="user",anc.states=gc_values[tree$node.label])
Error in if (x <= trans[1]) state <- names(trans)[1] else if (x >= trans[length(trans)]) state <- names(trans)[length(trans)] else { : missing value where TRUE/FALSE needed

I was able to make it work by doing the following:

anc.states = gc_values[tree$node.label]
names(anc.states) <- NULL
contMap(tree, gc_values[tree$tip.label],method="user",anc.states=anc.states)

It seems like the code is expecting that any ancestral sequences have names that are just integers represented as strings, even if node.label has other names:

else {
            if (is.null(names(anc.states))) 
                names(anc.states) <- 1:tree$Nnode + Ntip(tree)
            a <- anc.states[as.character(1:tree$Nnode + Ntip(tree))]
        }

Here, if names(anc.states) is not null, but also isn't equal to the integer-as-string names, then doing a <- anc.states[as.character(1:tree$Nnode + Ntip(tree))] creates a vector a that is filled with NA values.

Also, I found it a bit confusing that I had to split the values into different vectors for the tip nodes and the ancestral nodes.

[bredelings]

Here is the script and associated data. You can run it as ./GC.R A.fasta A.tree. It may have other bugs.

GC.gz

This is a tar.gz file, but github would not accept it if it was called GC.tgz