Remove recombinant lineages from time-scaled tree

PoonLab / covizu

Rapid analysis and visualization of coronavirus genome variation

https://filogeneti.ca/CoVizu/

MIT License

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Remove recombinant lineages from time-scaled tree #405

Closed ArtPoon closed 1 year ago

ArtPoon commented 2 years ago

I suspect this is being driven by Delta-Omicron recombinants (for example, lineage XS) - see screencap:

Since there are now enough recombinant lineages to distort the tree, we should probably exclude recombinant lineages from the tree. We still need to display beadplots for the recombinant lineages, so we have to come up with another way of allowing users to navigate to these. I think the simplest approach is to draw these lineages as independent branches above the tree:

This will break the current tree-drawing algorithm, though.

ArtPoon commented 2 years ago

Note that recombinant lineages always have an X prefix under the PANGO nomenclature system

ArtPoon commented 2 years ago

in progress

ArtPoon commented 2 years ago

@GopiGugan is implementing an additional div so that the original div containing the time-scaled tree can use the same relative coordinate system for drawing branches
for now let's just use earliest sample collection date for vertical ordering of recombinant lineages

ArtPoon commented 2 years ago

In progress, @GopiGugan resolving small bug involving tooltip

GopiGugan commented 2 years ago

ArtPoon commented 2 years ago

Let's focus on merging PR #409 before we work on incorporating this - thanks @GopiGugan !

ArtPoon commented 2 years ago