Add details panel for lineage mutations

[ArtPoon]

These can be presented as a table. See also #286

[ArtPoon]

Have to remember to credit Paul Gordon and his site for mutation metadata in this details panel

[ArtPoon]

This will enable us to abbreviate the number of mutations listed in the lineage tooltip

[ArtPoon]

Table should report the following for a selected lineage (do not modify for selected variant or bead?)

• mutation label (e.g., aa:orf1ab:P314L)
• mutation alias (?) or other information such as insertion sequence
• frequency in lineage
• phenotypic effects (from pokay)

[ArtPoon]

Might need to use some sort of letter or abbreviation encoding of phenotypic effects, and adding a corresponding legend above/below the details table.

[ArtPoon]

Let's make a new branch for backend and frontend development of this issue

[ArtPoon]

See branch mutationstable

[ArtPoon]

Need to modify backend to add mutation frequencies to dbstats.json file: https://github.com/PoonLab/covizu/blob/0691e41167294a3033b7a5a69db8cb24f562daaa/covizu/utils/batch_utils.py#L210-L229

[ArtPoon]

I think we can just modify this line in above code: common = [feat for feat, count in counts.items() if count/len(samples) >= 0.5] to common = dict([(feat, count/len(samples)) for feat, count in counts.items() if count/len(samples) >= 0.5])

[ArtPoon]

Need to update batch.py to handle dict instead of list

[ArtPoon]

Need to write a unit test for extracting mutation frequencies, with a specific test fixture

[bonnielu]

I've rewritten mut_annotation_edit.py to output a JSON file with the mutations as keys and phenotypes as values. Some mutations have ~20 phenotypes attributed to them. Not quite sure how to integrate this into our table — I was thinking of doing it with a tooltip but I'm open to suggestions right now!

[ArtPoon]

We can try a few things:

• be selective about what phenotypes to display in table
• do a many-to-one map of phenotypes to aggregate labels
• display phenotypes as "logos" - @ArtPoon to look for Sergei Pond's ObservableHQ notebook using logos to summarize evidence for positive selection at sites of SARS-CoV-2 genome as an example

[ArtPoon]

Shorten listing of mutations in tooltip when we implement the details table (#364)

[bonnielu]

The graph above shows the distribution of phenotype frequencies! Our current coverage, with 7 phenotypes in the legend, is about 70%.

[ArtPoon]

Thanks - so based on the barplot, the top N are:

• anthropozoonotic events - interesting, can use pangolin/bat icon
• pharmaceutical effectiveness - pill icon :-)
• convalescent plasma binding - what does this mean?
• vaccines plasma binding - can we combine this with convalescent plasma binding?
• reinfection - definitely of interest, not sure what an image would be
• virion structure - we can skip this
• transmissibility - obviously of interest
• T-cell evasion - can use a big "T"

[ArtPoon]

Need to provide some more informative text than "see more" for tooltip where number of mutations of lineage exceeds 5 (maybe display 10? display mutations derived from ancestral lineage?) Perhaps something more like "and 27 others"?

[bonnielu]

I've just had a sudden realization as to why the frequencies in the above graph are not adding up. The image I attached earlier had the 7 most frequent phenotypes removed (oops). This image below should represent the full set of phenotypes!

[ArtPoon]

• [ ] We need to check whether the changes to dbstats.json breaks the GISAID and VirusSeq front-ends before we can consider merging these changes to master. Checkout the respective branch and copy over JSON data from the mut_table branch to verify. We just need these other front ends to not break, i.e., tolerate changes to JSON formats.
• [ ] add attribution of new annotations JSON to Pokay
• [ ] get approval from Paul about new front-end

[ArtPoon]

@ArtPoon to convert clusters.json and return to @bonnielu for testing

[ArtPoon]

• [x] @bonnielu merge PR #380 from @dpannguyen
• [ ] @ArtPoon submit PR to merge mut_table branch into dev
• [ ] @GopiGugan go through dev to master merge process (manual update on BEVi, etc.)