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sa-lee / starmie

starmie: plotting and inference for population structure models :star2:

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Open sa-lee opened 8 years ago

sa-lee commented 8 years ago

Since structure model is the same thing as LDA (with 'documents' being samples, 'topics' as latent populations, and 'words' as genetic markers) we could use some of the ideas in http://nlp.stanford.edu/events/illvi2014/papers/sievert-illvi2014.pdf https://github.com/cpsievert/LDAvis to create some more informative/compelling plots

sa-lee commented 7 years ago

[x] plotMDS - mds plot using Jensen-Shannon metric or Structure output
[ ] plotRanks - bar plots ranking SNPs/microsatellites by cluster (need some kind of ranking meetric here)

Then our fully interactive plot that is like LDAvis

sa-lee commented 6 years ago

Other ideas: clustering tree ala http://lazappi.id.au/building-a-clustering-tree/ including uncertainty estimates in Q matrix from admixture