[Platform] Update metadata on study page and credible set page (#589)

opentargets · Dec 5, 2024 · e291bbb · e291bbb
1 parent e35a24c
commit e291bbb
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Showing 12 changed files with 296 additions and 235 deletions.
diff --git a/apps/platform/src/constants.js b/apps/platform/src/constants.js
@@ -341,7 +341,7 @@ export const variantConsequenceSource = {
   },
 };
 
-export const poulationMap = {
+export const populationMap = {
   fin: "Finish",
   afr: "African",
   nfe: "non-Finnish Europeans",

diff --git a/apps/platform/src/pages/CredibleSetPage/Profile.tsx b/apps/platform/src/pages/CredibleSetPage/Profile.tsx
@@ -53,7 +53,7 @@ function Profile({ studyLocusId, variantId, referenceAllele, alternateAllele }:
       variables={{ studyLocusId: studyLocusId, variantIds: [variantId] }}
       client={client}
     >
-      <ProfileHeader variantId={variantId} />
+      <ProfileHeader />
 
       <SummaryContainer>
         <VariantsSummary />

diff --git a/apps/platform/src/pages/CredibleSetPage/ProfileHeader.gql b/apps/platform/src/pages/CredibleSetPage/ProfileHeader.gql
@@ -49,6 +49,8 @@ fragment CredibleSetProfileHeaderFragment on credibleSet {
     publicationJournal
     pubmedId
     nSamples
+    cohorts
+    initialSampleSize
     studyType
     hasSumstats
     analysisFlags

diff --git a/apps/platform/src/pages/CredibleSetPage/ProfileHeader.tsx b/apps/platform/src/pages/CredibleSetPage/ProfileHeader.tsx
@@ -10,79 +10,22 @@ import {
   ClinvarStars,
   LabelChip,
   DetailPopover,
+  SummaryStatsTable,
+  DisplaySampleSize,
 } from "ui";
 import { Box, Typography } from "@mui/material";
 import CREDIBLE_SET_PROFILE_HEADER_FRAGMENT from "./ProfileHeader.gql";
-import { getStudyCategory } from "sections/src/utils/getStudyCategory";
 import { epmcUrl } from "../../utils/urls";
-import { credsetConfidenceMap, poulationMap } from "../../constants";
-import { v1 } from "uuid";
+import { credsetConfidenceMap, populationMap } from "../../constants";
 
-type ProfileHeaderProps = {
-  variantId: string;
-};
-
-const dicSummary = [
-  { id: "n_variants", label: "Total variants", tooltip: "Number of harmonised variants" },
-  { id: "n_variants_sig", label: "Significant variants", tooltip: "P-value significant variants" },
-  { id: "mean_beta", label: "Mean beta", tooltip: "Mean effect size across all variants" },
-  {
-    id: "gc_lambda",
-    label: "GC lambda",
-    tooltip: "Additive Genomic Control (GC) lambda indicating GWAS inflation",
-  },
-  {
-    id: "mean_diff_pz",
-    label: "Mean diff P-Z",
-    tooltip: "Mean difference between reported and calculated log p-values",
-  },
-  {
-    id: "se_diff_pz",
-    label: "SD diff P-Z",
-    tooltip: "Standard deviation of the difference between reported and calculated log p-values",
-  },
-];
-
-function SummaryStatsTable({ sumstatQCValues }: any) {
-  return (
-    <>
-      <Typography sx={{ fontSize: 16, fontWeight: 600, my: 1 }} variant="subtitle2">
-        Harmonised summary statistics
-      </Typography>
-      <table>
-        <tbody>
-          {dicSummary.map((sumstat: any) => {
-            const summStatValue = sumstatQCValues.find(
-              (v: any) => v.QCCheckName === sumstat.id
-            ).QCCheckValue;
-            return (
-              <tr key={v1()}>
-                <td>
-                  <Tooltip title={sumstat.tooltip} showHelpIcon>
-                    {sumstat.label}
-                  </Tooltip>
-                </td>
-                <Typography sx={{ textAlign: "right" }} component="td" variant="body2">
-                  {summStatValue}
-                </Typography>
-              </tr>
-            );
-          })}
-        </tbody>
-      </table>
-    </>
-  );
-}
-
-function ProfileHeader({ variantId }: ProfileHeaderProps) {
+function ProfileHeader() {
   const { loading, error, data } = usePlatformApi();
 
   // TODO: Errors!
   if (error) return null;
 
   const credibleSet = data?.credibleSet;
   const study = credibleSet?.study;
-  const studyCategory = study ? getStudyCategory(study.projectId) : null;
   const target = study?.target;
   const leadVariant = credibleSet?.locus.rows[0];
   const beta = leadVariant?.beta ?? credibleSet?.beta;
@@ -249,7 +192,7 @@ function ProfileHeader({ variantId }: ProfileHeaderProps) {
         <Typography variant="subtitle1" mt={0}>
           {study?.studyType.replace(/(qtl|gwas)/gi, match => match.toUpperCase())} Study
         </Typography>
-        {studyCategory !== "QTL" && (
+        {study?.studyType === "gwas" && (
           <>
             <Field loading={loading} title="Reported trait">
               {study?.traitFromSource}
@@ -276,7 +219,7 @@ function ProfileHeader({ variantId }: ProfileHeaderProps) {
             )}
           </>
         )}
-        {studyCategory === "QTL" && (
+        {study?.studyType !== "gwas" && (
           <>
             {target?.id && (
               <Field loading={loading} title="Affected gene">
@@ -308,18 +251,9 @@ function ProfileHeader({ variantId }: ProfileHeaderProps) {
             </PublicationsDrawer>
           </Field>
         )}
-        {study?.analysisFlags && (
-          <Field
-            loading={loading}
-            title={
-              <Tooltip title="Type of analysis" showHelpIcon>
-                Analysis
-              </Tooltip>
-            }
-          >
-            {study?.analysisFlags ? study.analysisFlags : "Not Available"}
-          </Field>
-        )}
+        <Field loading={loading} title="Analysis">
+          {study?.analysisFlags?.join(", ")}
+        </Field>
         <Field loading={loading} title="Summary statistics">
           {!study?.hasSumstats
             ? "Not Available"
@@ -330,21 +264,27 @@ function ProfileHeader({ variantId }: ProfileHeaderProps) {
               : "Available"
           }
         </Field>
-        <Field loading={loading} title="Sample size">
-          {study?.nSamples.toLocaleString()}
-        </Field>
-        <Box display="flex" sx={{ gap: 1 }}>
-          {/* LD Ancestries */}
-          {study?.ldPopulationStructure?.length > 0 &&
-            study.ldPopulationStructure.map(({ ldPopulation, relativeSampleSize }, index) => (
+        {study?.nSamples &&
+          <Field loading={loading} title="Sample size">
+            <DisplaySampleSize
+              nSamples={study.nSamples}
+              cohorts={study?.cohorts}
+              initialSampleSize={study?.initialSampleSize}
+            />
+          </Field>
+        }
+        {study?.ldPopulationStructure?.length > 0 &&
+          <Box display="flex" sx={{ gap: 1 }}>
+            {study.ldPopulationStructure.map(({ ldPopulation, relativeSampleSize }) => (
               <LabelChip
                 key={ldPopulation}
                 label={ldPopulation.toUpperCase()}
                 value={`${(relativeSampleSize * 100).toFixed(0)}%`}
-                tooltip={`LD reference population: ${poulationMap[ldPopulation]}`}
+                tooltip={`LD reference population: ${populationMap[ldPopulation]}`}
               />
             ))}
-        </Box>
+          </Box>
+        }
       </Box>
     </BaseProfileHeader >
   );

diff --git a/apps/platform/src/pages/StudyPage/Header.tsx b/apps/platform/src/pages/StudyPage/Header.tsx
@@ -29,7 +29,7 @@ function Header({
     if (diseases?.length) {
       traitLinks = (
         <XRefLinks
-          label="Trait"
+          label="Disease or phenotype"
           urlStem="../disease/"
           ids={diseases.map(d => d.id)}
           names={diseases.map(d => d.name)}

diff --git a/apps/platform/src/pages/StudyPage/Profile.tsx b/apps/platform/src/pages/StudyPage/Profile.tsx
@@ -68,7 +68,7 @@ function Profile({ studyId, studyType, projectId, diseases }: ProfileProps) {
       }}
       client={client}
     >
-      <ProfileHeader projectId={projectId} />
+      <ProfileHeader />
 
       <SummaryContainer>
         {studyType === "gwas" && (

diff --git a/apps/platform/src/pages/StudyPage/StudyProfileHeader.gql b/apps/platform/src/pages/StudyPage/StudyProfileHeader.gql
@@ -1,26 +1,40 @@
 fragment StudyProfileHeaderFragment on Gwas {
+  studyType
   publicationFirstAuthor
   publicationDate
   publicationJournal
   pubmedId
   traitFromSource
+  backgroundTraits {
+    id
+    name
+  }
+  diseases {
+    id
+    name
+  }
+  target {
+    id
+    approvedSymbol
+  }
   nSamples
   initialSampleSize
-  replicationSamples {
-    sampleSize
-    ancestry
-  }
   nCases
   nControls
   cohorts
   ldPopulationStructure {
     ldPopulation
     relativeSampleSize
   }
+  hasSumstats
+  sumstatQCValues {
+    QCCheckName
+    QCCheckValue
+  }
   qualityControls
   analysisFlags
-  discoverySamples {
-    sampleSize
-    ancestry
+  biosample {
+    biosampleId
+    biosampleName
   }
 }