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Characteristic mutations revision#432

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flaneuse wants to merge 27 commits intomasterfrom
char-muts-revision
Draft

Characteristic mutations revision#432
flaneuse wants to merge 27 commits intomasterfrom
char-muts-revision

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@flaneuse flaneuse commented Sep 2, 2021

  1. Convert table into bar graph
  2. Allow user to adjust the characteristic mutation threshold
  3. Create widget to look up the prevalence of a mutation within a lineage(s)
  4. Added sublineage heatmap for combined lineages
  5. Fixed Delta + lineage queries / reports

Screen Shot 2021-09-02 at 4 09 08 PM

2021-09-02: unfinished things that need adjustments from the backend queries of mutations within lineage(s) from either @gkarthik or @mindoftea:

  1. Switch https://api.outbreak.info/genomics/mutations-by-lineage?mutations=S:E484K,S:N501Y to be a bulk query (returns a list containing {S:E484K: [...], S:N501Y: [...]} and https://api.outbreak.info/genomics/mutations-by-lineage?mutations=S:E484K OR S:N501Y to be an OR query (returns {S:E484K,S:N501Y: [...]}
  2. Allow combination https://api.outbreak.info/genomics/mutations-by-lineage?mutations=S:E484K,S:N501Y&pangolin_lineage=AY.1%20OR%20AY.2
  3. Figure out what to do about lineage+mutation reports: if we lookup "prevalence of S:P681R in B.1.1.7 + S:E484K", is that what we want? How do we encode that?

@flaneuse flaneuse marked this pull request as draft September 2, 2021 23:58
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