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Allow aa branch label to be filtered to certain genes only, e.g. spike for SC2

Open corneliusroemer opened this issue 2 years ago • 1 comments

Sometimes it would be good for aa branch labels to be more selective. I'd sometimes like to see only AA substitutions that occur on the spike gene, instead of getting overwhelmed with dozens of numbers.

Spike signal (green) vs noise (black): image

It's really hard to mentally parse the long strings sometimes, for example ORF8: S67F can easily be mistaken for S: when glancing over at speed.

There two or more ways to implement this, if desired:

  • Add an extra branch/tip label property Spike aa to the tree during, through a script or maybe during augur refine
  • Add logic for auspice to be able to offer filtered gene aa labels

corneliusroemer avatar Sep 17 '21 09:09 corneliusroemer

Currently, auspice has no special logic around branch labels, these are being supplied as a specific branch label in the dataset JSON. As such, I would recommend we modify the ncov pipeline to produce a spike-specific branch labelling.

jameshadfield avatar Sep 20 '21 00:09 jameshadfield