Coloring by nt shows non-N bases, but amino acid is showing X where unmutated
AngieHinrichs opened this issue · comments
Hi Theo! Viewing a tree from @iqbal-lab, when I choose Color by: Genotype and it defaults to S:484, the unmutated parts of the tree are all grey and mouseover shows 'X' for the grey sequences:
It's even more striking for a position like 377 - almost the entire tree is grey. But if I color by nucleotide at the same positions (22691-22693, thanks for codon2nucleotide 😃) then all nucleotide bases are colored correctly from the root of the tree.
Hey so unfortunately when I overhauled GenBank import in taxoniumtools a few months back to deal with compound features I broke the annotation of the root node without noticing. This was recently fixed https://github.com/theosanderson/taxonium/releases/tag/v2.0.111 but probably too late for this tree. Really sorry for the inconvenience. Please let me know if it persists in any new trees.
Ah, thanks Theo, so this should just go away when they update taxoniumtools and re-run. I'll close this now and reopen if that doesn't do the trick.
Thanks Theo, can confirm that the tree was made using taxoniumtools 2.0.110. If I rerun with 2.0.111 then it's mostly fixed.
But I am getting a glitchy display issue where depending on zoom level everything turns grey. Maybe related? I don't know. I've not seen this happen before.
Two screenshots attached of the same session, only difference between them is I used the mouse wheel to zoom in/out. Running on taxonium.org/M1 mac/safari.
@martinghunt - huh! that's a new one to me.
Some questions:
- Can you get this to happen at cov2tree.org?
- I've made some changes to some bits of (web) Taxonium lately to add new colour customisability. https://cov2tree-9k82lpuou-theosanderson.vercel.app/ is a version before those changes - does that have the same bug? If not it might be a temporary fallback for you
- Is this generally very reproducible, i.e. does it happen every time?
If it doesn't happen on cov2tree.org please could you send a file where it happens over to theo@theo.io - dropboxed or whatever?
OK I can reproduce this - doesn't happen with web taxonium but does with a JSONL
It indeed appears that https://cov2tree-9k82lpuou-theosanderson.vercel.app/ is unaffected if that helps in the short term
Thank you @theosanderson, yes https://cov2tree-9k82lpuou-theosanderson.vercel.app/ is working perfectly for me. Will use that for now.
Just using this ticket for notes to myself for a bit:
- easiest way to reproduce is zoom right in when not on "genotype" mode, then switch to genotype mode. works for cov2tree too.
- relates to the colorCache in useColorBy - if you disable caching it stops happening
- presumably there is an initial point where it can't find parents and so cache gets set to "X". that initial point where it can't find parents shouldn't happen.
Hopefully a fix is rolling out, preview at https://cov2tree-git-fix-genotype-theosanderson.vercel.app/ . If it doesn't fix the issue please let me know. Thanks for reporting
Thanks for fixing so fast! That preview is working perfectly for me
Awesome - (should be same on main site)