I would like to use ggtree to annotate & visualize part of the taxonomy tree provided by NCBI.

The NCBI taxnonomy information is provided in a simple 2-column format:  "<taxid>   <parent taxid>"

(see file "nodes.dmp"  within the TAR  ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz )

However, all of the data import options for ggtree seem geared toward specialized software.   How can I import this "custom" node-association information NCBI taxonomy data and make a suitable tree for ggtree?

ggtree not only work for software output, but also with standard tree format, including newick, nexus, nhx, phylip, jplace.

It also work with S3/S4 tree objects generated by other packages, including phylo and multiPhylo (ape), obkData (OutbreakTools) and phyloseq (phyloseq).

NCBI taxonomy data is not tree file and we need to build a tree (newick or nexus) from the data before it can be visualized using ggtree.

To my knowledge, there is no R package can do this task. After searching it in github, I found a python script, https://github.com/bendmorris/taxiphy, that can read NCBI taxonomy and generate tree file in newick format. The output file can be parsed in R and visualized using ggtree.

For future visitors, consider using ETE's NCBI Taxonomy function to write the tree with your desired nodes and then later draw/manipulate it using ggtree.

http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html