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malariagen / malariagen-data-python

Analyse MalariaGEN data from Python
https://malariagen.github.io/malariagen-data-python/latest/
MIT License
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Chord diagram to visualise haplotype sharing #458

Open alimanfoo opened 9 months ago

alimanfoo commented 9 months ago

Related to #457, another possibility for visualising haplotype sharing to infer adaptive gene flow would be a chord diagram. This could either plot individual haplotypes around the circumference, or plot cohorts with line thickness proportional to number of shared haplotypes.

image

alimanfoo commented 9 months ago

Also this could be efficient as we just need to compute identical haplotype sharing, no need to do the full pairwise distance calculation. So this can be done via hashing of haplotypes in roughly O(n).