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YuLab-SMU / ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees
https://yulab-smu.top/treedata-book/
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plotting big tree error #563

Open Asa12138 opened 1 year ago

Asa12138 commented 1 year ago

I meet some errors when I plot a Phylogenetic tree with 3874 tips and 2850 internal nodes.

> aa

Phylogenetic tree with 3874 tips and 2850 internal nodes.

Tip labels:
  s__Scortechinia_acanthostroma, s__Tympanopsis_confertula, s__Bradyrhizobium_erythrophlei, s__Bertia_moriformis, s__Bradyrhizobium_sp., s__Chaetosphaerella_phaeostroma, ...
Node labels:
  r__root, d__Eukaryota, d__Bacteria, d__Archaea, d__Viruses, k__Fungi, ...

Unrooted; includes branch lengths.

>ggtree(aa) 

Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) : 
  long vectors not supported yet: /Volumes/Builds/R4/R-4.1.2/src/include/Rinlinedfuns.h:537

I use the latest version of R and ggtree, I also try different Platform and version but bugs still there.

I test this code:

ggtree(rtree(5000))

It works well, so maybe not the number of tips but label of tree cause this problem?

Thanks if you can help me.

Asa12138 commented 1 year ago

。。。I spent lots of time and finally find the reason. because a special scientific name called Paracoccus, this genus have two totally different lineage from NCBI taxonomy.

d__Eukaryota k__Metazoa p__Arthropoda c__Insecta o__Hemiptera f__Pseudococcidae g__Paracoccus
d__Bacteria k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodobacterales f__Rhodobacteraceae g__Paracoccus

so this tree topology structure is not right, this is very strange.