Open ammaraziz opened 1 month ago
I am happy to roll back to an R/ggtree version that works, if you could provide guidance which to test?
The taxa1
and taxa2
should be the tip.label
or node
number of tree
.
> tree
'treedata' S4 object'.
...@ phylo:
Phylogenetic tree with 8 tips and 4 internal nodes.
Tip labels:
ADH2, ADH1, ADHY, ADHX, ADH4, ADH3, ...
Rooted; includes branch lengths.
with the following features available:
'V1', 'B', 'D', 'S'.
# The associated data tibble abstraction: 12 × 7
# The 'node', 'label' and 'isTip' are from the phylo tree.
node label isTip V1 B D S
<int> <chr> <lgl> <dbl> <dbl> <chr> <chr>
1 1 ADH2 TRUE NA NA NA human
2 2 ADH1 TRUE NA NA NA human
3 3 ADHY TRUE NA NA NA nematode
4 4 ADHX TRUE NA NA NA insect
5 5 ADH4 TRUE NA NA NA yeast
6 6 ADH3 TRUE NA NA NA yeast
7 7 ADH2 TRUE NA NA NA yeast
8 8 ADH1 TRUE NA NA NA yeast
9 9 NA FALSE NA NA N NA
10 10 NA FALSE NA NA N metazoa
# ℹ 2 more rows
# ℹ Use `print(n = ...)` to see more rows
ggtree(tree, layout='circluar') + geom_tiplab() + geom_taxalink(taxa1=2, taxa2=4, hratio=3)
ggtree(tree) + geom_tiplab() + geom_taxalink(taxa1='ADHY', taxa2='ADH3')
Please refer to the help information of geom_taxalink
using ?geom_taxalink
Prerequisites
Describe you issue
From the ggtree book example here:
Produces this error:
I have also tried using mapping:
Error:
Newly installed R4.4 and latest ggtree.
Software Versions