Genetics Variant page review

[prashantuniyal02]

General

• Displaying numeric data:
  • use numeric option in appropriate table columns (right-align, monospace font).
  • format large integers with commas wherever appropriate
  • round decimals wherever appropriate
• Fix sorting where possibility of NA in column - comparator function should return 0 when both values nullish; nullish values should be larger/smaller than all other values dependent on intuitive sort direction for column

Variant page

Header:

Widget order? In silico (V) > VEP (V2G) > ClinVar (V2D) > Uniprot (V2D) > GWAS (V2L2D) > molQTL (V2G) > Pharmacogenetics (V2D2Dr)

Metadata:

• most severe consequence gene(s)? [May be in 2.0]
• Allelic frequency. Visualisation is odd. Numbers are relevant even on a log scale. Shall we be able to change from natural to log scale? Toggle?

Overall about widgets:

• Save horizontal space [review data & number of rows]
• Make sure top 25 rows is not an issue anywhere - pagination issues
• Should we reuse the concept from Genetics of representing "V" "V-G" "V-D" in the top-right of the widgets? [not to be used in genetics widgets]
• Categorical filter of columns would help in many places (Table component work). e.g. Affected tissue / cell etc.

In silico predictors:

• Description: [to be discussed offline]
• Tooltip for methods
• Format methods name
• Ideas?
• color ranges would need to be based on some information - @DSuveges to talk to FE #3503

Variant effect predictor:

• Description: [to be discussed offline]
• Compress Aminoacid change + Coding Change + Uniprot accession somewhere. Probably predicted consequence column when not NA
• missense variant ( P19438 cGg/cAg, R121Q )
• check extreme cases where there a more functional consequences

ClinVar: good

Uniprot variants: good

GWAS Credible sets and molQTL credible sets:

• Description: [to be discussed offline]
• Confidence (star system)
• Enhance [view] button UI. Title "View" and chavron?
• LD column? Drop [keep it in credible set visualisation)
• 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)
• To add the condition

PheWAS plot:

• to be scoped

[buniello]

Adding these points from #3597

VEP

Column headers need clearer definitions for better understanding

When downloading VEP data, users request: 1. Uniprot links 2. Chromosome and position for genes

In-silico predictors

Suggestion: adding hyperlinks or hover text to explain prediction methods. For example, SIFT=0 means "deleterious," which is opposite to PolyPhen where a score closer to 1 indicates deleterious