[Platform]: consequence column added to credset variants widget (#552)

opentargets · Nov 22, 2024 · bf7e68a · bf7e68a
1 parent c859339
commit bf7e68a
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Showing 3 changed files with 30 additions and 1 deletion.
diff --git a/packages/sections/src/credibleSet/Variants/Body.tsx b/packages/sections/src/credibleSet/Variants/Body.tsx
@@ -6,13 +6,18 @@ import { definition } from ".";
 import Description from "./Description";
 import VARIANTS_QUERY from "./VariantsQuery.gql";
 import { mantissaExponentComparator, variantComparator } from "../../utils/comparators";
+import { identifiersOrgLink } from "../../utils/global";
 
 type getColumnsType = {
   leadVariantId: string;
   leadReferenceAllele: string;
   leadAlternateAllele: string;
 };
 
+function formatVariantConsequenceLabel(label) {
+  return label.replace(/_/g, " ");
+}
+
 function getColumns({ leadVariantId, leadReferenceAllele, leadAlternateAllele }: getColumnsType) {
   return [
     {
@@ -132,6 +137,25 @@ function getColumns({ leadVariantId, leadReferenceAllele, leadAlternateAllele }:
         return logBF.toPrecision(3);
       },
     },
+    {
+      id: "variant.mostSevereConsequence.label",
+      label: "Predicted consequence",
+      tooltip: "Most severe consequence of the variant. Source: Ensembl VEP",
+
+      renderCell: ({ variant }) => {
+        const mostSevereConsequence = variant?.mostSevereConsequence
+        if (!mostSevereConsequence) return naLabel;
+        const displayElement = (
+            <Link external to={identifiersOrgLink("SO", mostSevereConsequence.id.slice(3))}>
+              {formatVariantConsequenceLabel(mostSevereConsequence.label)}
+            </Link>
+        );
+        return displayElement;
+      },
+      exportValue: ({ variant }) => {
+        return variant?.mostSevereConsequence.label
+      },
+    },
   ];
 }
 

diff --git a/packages/sections/src/credibleSet/Variants/VariantsQuery.gql b/packages/sections/src/credibleSet/Variants/VariantsQuery.gql
@@ -12,6 +12,10 @@ query VariantsQuery($studyLocusId: String!) {
           position
           referenceAllele
           alternateAllele
+          mostSevereConsequence {
+            id
+            label
+          }
         }
         pValueMantissa
         pValueExponent

diff --git a/packages/sections/src/variant/VariantEffectPredictor/Body.tsx b/packages/sections/src/variant/VariantEffectPredictor/Body.tsx
@@ -8,6 +8,7 @@ import { naLabel } from "../../constants";
 import { identifiersOrgLink } from "../../utils/global";
 import VARIANT_EFFECT_PREDICTOR_QUERY from "./VariantEffectPredictorQuery.gql";
 
+
 function formatVariantConsequenceLabel(label) {
   return label.replace(/_/g, " ");
 }
@@ -81,7 +82,7 @@ const columns = [
   {
     id: "variantConsequences.label",
     label: "Predicted consequence",
-    renderCell: ({ variantConsequences, aminoAcidChange, codons, uniprotAccessions }) => {
+    renderCell: ({ variantConsequences, aminoAcidChange, codons }) => {
       if (!variantConsequences?.length) return naLabel;
       let displayElement = variantConsequences.map(({ id, label }, i, arr) => (
         <Fragment key={id}>