Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Characteristic mutations revision #432

Draft
wants to merge 27 commits into
base: master
Choose a base branch
from
Draft

Conversation

flaneuse
Copy link
Collaborator

@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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant