[Platform]: Variant page review

[chinmehta]

[Platform]: Variant page review

Description

• Widget order
• Compress Aminoacid change + Coding Change + Uniprot accession columns. When aminoacid change is not NA show within the predicted consequence column: missense variant [R121Q]^? Tooltip: Uniprot accession: [P19438](Link to uniprot using identifiers.org)
• Confidence (star system)
• Enhance [view] button UI. Title "View" and chavron?
• LD column? Drop
• Top L2G - (update to match the API )
• L2G score (continuous filled bar)
• Allow sorting by numeric columns (incl. posterior probability) (default p-value)
• Affected tissue/cell: to show actual tissue label (not the ID) (e.g. blood plasma)
• molQTL source : Source [Open Targets](link to Open targets homepage)

Issue: opentargets/issues#3601 , opentargets/issues#3616
Deploy preview: https://deploy-preview-524--ot-platform-partner.netlify.app/

Type of change

• New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce.

• Test A
• Test B

Checklist:

• I have commented my code, particularly in hard-to-understand areas
• My changes generate no new warnings
• I have made corresponding changes to the documentation

[d0choa]

Some feedback. Feel free to decide what goes here and what goes in future PRs. There is a benefit on merging this the moment there is a favourable technical review, as it has a lot of good things and rescues the credible set widgets

• Widget order -> Great
• Compress Aminoacid change + Coding Change + Uniprot accession columns - Changes look great but there is one thing missing. If the Amino acid change column is non-NA we want to place the label in the predicted consequence column. E.g. missense variant R121Q [cGg/cAg]? in this variant page. After this change, you can drop the Amino acid change column and it will remove a lot of useless N/As.
• Confidence (star system) - Works perfectly. Can we allow sorting by this column?
• Enhance [view] button UI. I guess this is WIP?
• LD column? Done
• Top L2G - (update to match the API ) - Works well - It's possible that the top L2G is N/A in some cases. Make sure you handle that.
• L2G score (continuous filled bar) - I like the UI. We could add a color gradient if we feel we need it. Great for now.
• Allow sorting by numeric columns (incl. posterior probability) (default p-value) - Beta in the molQTL widget is missing.
• Affected tissue/cell: to show actual tissue label (not the ID) (e.g. blood plasma)
• molQTL source : Source [Open Targets](link to Open targets homepage)

Remember to add the condition to the molQTL table. It's a very easy change.

      study {
        studyId
        studyType
        target {
          id
          approvedSymbol
        }
        biosample {
          biosampleId
          biosampleName
        }
        condition
      }

Also look at the sorting of the VEP widget which was originally missing from the spec

[d0choa]

There is a bug in the VEP widget:

The Distance to Footprint column is incorrectly showing N/A when values are 0.

Example page:
https://deploy-preview-524--ot-platform-partner.netlify.app/variant/12_6333477_C_T

        {
          "variantConsequences": [
            {
              "id": "SO:0001627",
              "label": "intron_variant"
            }
          ],
          "aminoAcidChange": null,
          "uniprotAccessions": [
            "P08887",
            "A0N0L5"
          ],
          "codons": null,
          "distanceFromFootprint": 0,
          "distanceFromTss": 48445,
          "target": {
            "id": "ENSG00000160712",
            "approvedSymbol": "IL6R"
          },
          "impact": "MODIFIER",
          "consequenceScore": 0.10000000149011612,
          "transcriptIndex": 1,
          "transcriptId": "ENST00000368485",
          "lofteePrediction": null,
          "siftPrediction": null,
          "polyphenPrediction": null
        }

Let me know if this is a more widespread issue and we can open a ticket for it