nextstrain/ncov

ENH: Add S1 mutations, reversion count and other branch colorings

corneliusroemer opened this issue · 0 comments

Context
I found S1 mutations a super useful coloring in the pre-Omicron days.

Unfortunately, Omicron has so many S1 mutations now that new S1 mutations are no longer identifiable through this coloring.

Description
It would be great if we could add a few colorings to ncov that are at branch level.

This would allow more informative tree scanning/browsing by coloring at a local level - where granularity is not hidden through signal/noise issues.

Examples

While we're at it - we may want to add other things as branch colorings, like number of reversions on a branch, to quickly be able to spot bad branches.

I could imagine that there are other metrics where a branch-level delta coloring would be great.

In fact, we may even want to think about integrating a coloring "delta" mode into Auspice. Anything that gets accumulated could also be displayed in delta/diff branch mode. @jameshadfield

Possible solution

Add a script that calculates branch diffs based on cumulative information already present in the auspice.json - post processing of the auspice.json tree.

Alternatively, this could be a separate node-data.json input.