Merge pull request #443 from bcgsc/feat/DEVSU-2244-cd8t-percentile-vi…

…sibility-toggle DEVSU-2244 CD8+ T Cell Percentile Visibility Toggle
bcgsc · Mar 28, 2024 · d8929c8 · d8929c8
2 parents df83ea3 + 4f6af23
commit d8929c8
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Showing 5 changed files with 58 additions and 9 deletions.
diff --git a/app/common.d.ts b/app/common.d.ts
@@ -321,6 +321,7 @@ type ImmuneType = {
   pedsPercentile: number | null;
   pedsScore: number | null;
   pedsScoreComment: string | null;
+  percentileHidden: boolean;
 } & RecordDefaults;
 
 type MicrobialType = {

diff --git a/app/components/TumourSummaryEdit/index.scss b/app/components/TumourSummaryEdit/index.scss
@@ -9,6 +9,11 @@
 
   &__check-box {
     color: gray;
-    padding-top: 2px;
+    margin-top: -12px;
+    font-size: 2;
   }
+}
+
+.checkbox-label {
+  font-size: 10pt;
 }
diff --git a/app/components/TumourSummaryEdit/index.tsx b/app/components/TumourSummaryEdit/index.tsx
@@ -87,6 +87,7 @@ const TumourSummaryEdit = ({
       setNewTCellCd8Data({
         score: tCellCd8.score,
         percentile: tCellCd8.percentile,
+        percentileHidden: tCellCd8.percentileHidden,
         pedsScore: tCellCd8.pedsScore,
         pedsPercentile: tCellCd8.pedsPercentile,
         pedsScoreComment: tCellCd8.pedsScoreComment,
@@ -129,6 +130,14 @@ const TumourSummaryEdit = ({
     setTCellCd8Dirty(true);
   }, []);
 
+  const handleTCellCd8PercentileVisibleChange = useCallback(({ target: { checked, name } }) => {
+    setNewTCellCd8Data((prevVal) => ({
+      ...prevVal,
+      [name]: checked,
+    }));
+    setTCellCd8Dirty(true);
+  }, []);
+
   const handlePedsCd8tChange = useCallback(({ target: { value, name } }) => {
     setNewTCellCd8Data((cd8t) => ({
       ...cd8t,
@@ -454,6 +463,27 @@ const TumourSummaryEdit = ({
         fullWidth
         type="number"
       />
+      <FormControlLabel
+        className="tumour-dialog__check-box"
+        control={(
+          <Checkbox
+            size="small"
+            icon={<Visibility />}
+            checkedIcon={<VisibilityOff />}
+            checked={newTCellCd8Data?.percentileHidden}
+            name="percentileHidden"
+            onChange={handleTCellCd8PercentileVisibleChange}
+            sx={{
+              color: 'default',
+              '&.Mui-checked': {
+                color: pink[800],
+              },
+              marginLeft: 1,
+            }}
+          />
+        )}
+        label={<div className="checkbox-label">Show/Hide CD8+ Percentile</div>}
+      />
       <TextField
         className="tumour-dialog__text-field"
         label="Pediatric CD8+ T Cell Score"
@@ -489,7 +519,7 @@ const TumourSummaryEdit = ({
         type="text"
       />
     </>
-  ), [newTCellCd8Data?.score, newTCellCd8Data?.percentile, newTCellCd8Data?.pedsScore, newTCellCd8Data?.pedsPercentile, newTCellCd8Data?.pedsScoreComment, handleTCellCd8Change, report.patientInformation.caseType, handlePedsCd8tChange, handlePedsCd8tCommentChange]);
+  ), [newTCellCd8Data?.score, newTCellCd8Data?.percentile, newTCellCd8Data?.percentileHidden, newTCellCd8Data?.pedsScore, newTCellCd8Data?.pedsPercentile, newTCellCd8Data?.pedsScoreComment, handleTCellCd8Change, handleTCellCd8PercentileVisibleChange, report.patientInformation.caseType, handlePedsCd8tChange, handlePedsCd8tCommentChange]);
 
   const mutBurDataSection = useMemo(() => (
     <>
@@ -564,6 +594,7 @@ const TumourSummaryEdit = ({
         className="tumour-dialog__check-box"
         control={(
           <Checkbox
+            size="small"
             icon={<Visibility />}
             checkedIcon={<VisibilityOff />}
             checked={newTmburMutData?.tmbHidden}
@@ -574,10 +605,11 @@ const TumourSummaryEdit = ({
               '&.Mui-checked': {
                 color: pink[800],
               },
+              marginLeft: 1,
             }}
           />
         )}
-        label="Show/Hide TMB Score"
+        label={<div className="checkbox-label">Show/Hide TMB Information</div>}
       />
     </>
   ), [newTmburMutData?.genomeSnvTmb, newTmburMutData?.genomeIndelTmb, newTmburMutData?.adjustedTmb, newTmburMutData?.adjustedTmbComment, newTmburMutData?.tmbHidden, handleTmburChange, handleAdjustedTmbCommentChange, handleAdjustedTmbVisibleChange]);

diff --git a/app/views/ReportView/components/GenomicSummary/index.tsx b/app/views/ReportView/components/GenomicSummary/index.tsx
@@ -194,9 +194,9 @@ const GenomicSummary = ({
       let tCell: null | string;
       if (tCellCd8 && typeof tCellCd8.score === 'number') {
         if (tCellCd8.pedsScore) {
-          tCell = `${tCellCd8.pedsScore} ${tCellCd8.pedsPercentile ? `(${tCellCd8.pedsPercentile}%)` : ''}`;
+          tCell = `${tCellCd8.pedsScore} ${tCellCd8.pedsPercentile && !tCellCd8.percentileHidden ? `(${tCellCd8.pedsPercentile}%)` : ''}`;
         } else {
-          tCell = `${tCellCd8.score} ${tCellCd8.percentile ? `(${tCellCd8.percentile}%)` : ''}`;
+          tCell = `${tCellCd8.score} ${tCellCd8.percentile && !tCellCd8.percentileHidden ? `(${tCellCd8.percentile}%)` : ''}`;
         }
       } else {
         tCell = null;

diff --git a/app/views/ReportView/components/RapidSummary/index.tsx b/app/views/ReportView/components/RapidSummary/index.tsx
@@ -314,10 +314,11 @@ const RapidSummary = ({
 
     let tCell: null | string;
     if (tCellCd8 && typeof tCellCd8.score === 'number') {
-      if (!!tCellCd8.pedsScore && !!tCellCd8.pedsPercentile) {
-        tCell = `${tCellCd8.pedsScore} ${tCellCd8.pedsPercentile ? `(${tCellCd8.pedsPercentile}%)` : ''}`;
+      if (tCellCd8.pedsScore) {
+        tCell = `${tCellCd8.pedsScore} ${tCellCd8.pedsPercentile && !tCellCd8.percentileHidden ? `(${tCellCd8.pedsPercentile}%)` : ''}`;
+      } else {
+        tCell = `${tCellCd8.score} ${tCellCd8.percentile && !tCellCd8.percentileHidden ? `(${tCellCd8.percentile}%)` : ''}`;
       }
-      tCell = `${tCellCd8.score} ${tCellCd8.percentile ? `(${tCellCd8.percentile}%)` : ''}`;
     } else {
       tCell = null;
     }
@@ -356,6 +357,15 @@ const RapidSummary = ({
           tCellCd8?.pedsScore ? 'Pediatric CD8+ T Cell Score' : 'CD8+ T Cell Score',
         value: tCell,
       },
+      {
+        term: 'Pediatric CD8+ T Cell Comment',
+        value:
+          tCellCd8?.pedsScoreComment ? tCellCd8?.pedsScoreComment : null,
+      },
+      {
+        term: 'Mutation Burden',
+        value: primaryBurden && primaryBurden.totalMutationsPerMb !== null && (!tmburMutBur?.adjustedTmb || tmburMutBur.tmbHidden === true) ? `${primaryBurden.totalMutationsPerMb} Mut/Mb` : null,
+      },
       {
         term: 'SV Burden (POG Average)',
         value: svBurden,
@@ -376,7 +386,8 @@ const RapidSummary = ({
         value: msiStatus,
       },
     ]);
-  }, [microbial, primaryBurden, tmburMutBur, report.m1m2Score, report.sampleInfo, report.tumourContent, report.captiv8Score, tCellCd8]);
+  }, [microbial, primaryBurden, tmburMutBur, report.m1m2Score, report.sampleInfo, report.tumourContent, tCellCd8.percentile, tCellCd8.score, report.captiv8Score,
+    tCellCd8.percentileHidden, tCellCd8, tCellCd8.pedsScoreComment, tmburMutBur.adjustedTmb, tmburMutBur.tmbHidden, tCellCd8.pedsScore, tCellCd8.pedsPercentile]);
 
   const handlePatientEditClose = useCallback((
     newPatientData: PatientInformationType,