Merge pull request #3705 from adamabeshouse/8501-driver

Add driver annotation to download tab
cBioPortal · Apr 13, 2021 · 0b206b1 · 0b206b1
2 parents 12b6502 + 7ba8e01
commit 0b206b1
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Showing 9 changed files with 64 additions and 7 deletions.
diff --git a/...sclc_tcga_broad_2016_for_query_egfr:_mut=t790m_amp_element_chrome_1600x1000.png b/...sclc_tcga_broad_2016_for_query_egfr:_mut=t790m_amp_element_chrome_1600x1000.png
diff --git a/...d_2016_with_cdkn2a_mdm2_and_merged_track_mdm4_tp53_element_chrome_1600x1000.png b/...d_2016_with_cdkn2a_mdm2_and_merged_track_mdm4_tp53_element_chrome_1600x1000.png
diff --git a/..._tab_-_nsclc_tcga_broad_2016_with_overlapping_tp53_element_chrome_1600x1000.png b/..._tab_-_nsclc_tcga_broad_2016_with_overlapping_tp53_element_chrome_1600x1000.png
diff --git a/...nce/download_tab_-_nsclc_tcga_broad_2016_with_tp53_element_chrome_1600x1000.png b/...nce/download_tab_-_nsclc_tcga_broad_2016_with_tp53_element_chrome_1600x1000.png
diff --git a/src/pages/resultsView/download/CaseAlterationTable.tsx b/src/pages/resultsView/download/CaseAlterationTable.tsx
@@ -27,12 +27,17 @@ import { insertBetween } from 'shared/lib/ArrayUtils';
 export interface ISubAlteration {
     type: string;
     value: number;
+    putativeDriver?: boolean;
 }
 
 export interface IOqlData {
     geneSymbol: string;
     sequenced: boolean;
-    mutation: { proteinChange: string; isGermline: boolean }[];
+    mutation: {
+        proteinChange: string;
+        isGermline: boolean;
+        putativeDriver: boolean;
+    }[];
     fusion: string[];
     cna: ISubAlteration[];
     mrnaExp: ISubAlteration[];
@@ -78,7 +83,9 @@ type RenderGenerator<T> = {
 function mutationMapper(forDownload?: boolean) {
     const renderMutation = (d: IOqlData['mutation'][0]) => {
         if (forDownload) {
-            return `${d.proteinChange}${d.isGermline ? ' [germline]' : ''}`;
+            return `${d.proteinChange}${d.isGermline ? ' [germline]' : ''}${
+                d.putativeDriver ? ' (driver)' : ''
+            }`;
         } else {
             return (
                 <span>
@@ -88,6 +95,11 @@ function mutationMapper(forDownload?: boolean) {
                             Germline
                         </span>
                     )}
+                    {d.putativeDriver && (
+                        <span className={proteinChangeStyles.driver}>
+                            (Driver)
+                        </span>
+                    )}
                 </span>
             );
         }
@@ -97,6 +109,26 @@ function mutationMapper(forDownload?: boolean) {
         alterationData.map(renderMutation);
 }
 
+function cnaMapper(forDownload?: boolean) {
+    const renderCna = (d: IOqlData['cna'][0]) => {
+        if (forDownload) {
+            return `${d.type}${d.putativeDriver ? ' (driver)' : ''}`;
+        } else {
+            return (
+                <span>
+                    <span>{d.type}</span>
+                    {d.putativeDriver && (
+                        <span className={proteinChangeStyles.driver}>
+                            (Driver)
+                        </span>
+                    )}
+                </span>
+            );
+        }
+    };
+    return (alterationData: IOqlData['cna']) => alterationData.map(renderCna);
+}
+
 export function generateOqlValue(
     data: IOqlData,
     alterationType: string,
@@ -144,7 +176,7 @@ export function generateOqlValue(
                 label: 'CNA',
                 getAlterationData: (oqlData: IOqlData) => oqlData.cna,
                 isNotProfiled: (oqlData: IOqlData) => oqlData.isCnaNotProfiled,
-                getValues: subAlterationMapper,
+                getValues: cnaMapper(forDownload),
             };
             break;
         case 'EXP':

diff --git a/src/pages/resultsView/download/DownloadUtils.spec.ts b/src/pages/resultsView/download/DownloadUtils.spec.ts
@@ -476,8 +476,16 @@ describe('DownloadUtils', () => {
             assert.deepEqual(
                 oqlData.mutation,
                 [
-                    { proteinChange: 'G598A', isGermline: true },
-                    { proteinChange: 'G239C', isGermline: false },
+                    {
+                        proteinChange: 'G598A',
+                        isGermline: true,
+                        putativeDriver: true,
+                    },
+                    {
+                        proteinChange: 'G239C',
+                        isGermline: false,
+                        putativeDriver: false,
+                    },
                 ],
                 'mutation data is correct for the sample with mutation and fusion data'
             );
@@ -867,8 +875,16 @@ describe('DownloadUtils', () => {
             assert.deepEqual(
                 caseAlterationData[0].oqlData['EGFR'].mutation,
                 [
-                    { proteinChange: 'G598A', isGermline: true },
-                    { proteinChange: 'G239C', isGermline: false },
+                    {
+                        proteinChange: 'G598A',
+                        isGermline: true,
+                        putativeDriver: true,
+                    },
+                    {
+                        proteinChange: 'G239C',
+                        isGermline: false,
+                        putativeDriver: false,
+                    },
                 ],
                 'mutation data is correct for the sample key UC0wMDAwMzc4LVQwMS1JTTM6bXNrX2ltcGFjdF8yMDE3'
             );

diff --git a/src/pages/resultsView/download/DownloadUtils.ts b/src/pages/resultsView/download/DownloadUtils.ts
@@ -75,6 +75,7 @@ export function generateOqlData(
                     cnaAlterations.push({
                         type: alterationSubType,
                         value: alteration.value,
+                        putativeDriver: alteration.putativeDriver,
                     });
                     alterationTypes.push('CNA');
                 }
@@ -105,6 +106,7 @@ export function generateOqlData(
                     mutation.push({
                         proteinChange: alteration.proteinChange,
                         isGermline: !isNotGermlineMutation(alteration),
+                        putativeDriver: alteration.putativeDriver,
                     });
                     alterationTypes.push('MUT');
                 }

diff --git a/src/shared/components/mutationTable/column/proteinChange.module.scss b/src/shared/components/mutationTable/column/proteinChange.module.scss
@@ -8,3 +8,9 @@
     font-size: x-small;
     margin-left: 5px;
 }
+
+.driver {
+    font-weight: normal;
+    font-style: italic;
+    margin-left: 5px;
+}
diff --git a/src/shared/components/mutationTable/column/proteinChange.module.scss.d.ts b/src/shared/components/mutationTable/column/proteinChange.module.scss.d.ts
@@ -1,4 +1,5 @@
 declare const styles: {
+  readonly "driver": string;
   readonly "germline": string;
   readonly "proteinChange": string;
 };