Merge remote-tracking branch 'origin/master' into release-1.13.0

cBioPortal · May 10, 2018 · 5beacf4 · 5beacf4
2 parents d0f8387 + 5bd9a3e
commit 5beacf4
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Showing 5 changed files with 28 additions and 26 deletions.
diff --git a/...ests/screenshots/reference/no_session_mutation_tab_element_chrome_1600x1000.png b/...ests/screenshots/reference/no_session_mutation_tab_element_chrome_1600x1000.png
diff --git a/...d-tests/screenshots/reference/session_mutation_tab_element_chrome_1600x1000.png b/...d-tests/screenshots/reference/session_mutation_tab_element_chrome_1600x1000.png
diff --git a/src/pages/resultsView/mutation/MutationMapper.tsx b/src/pages/resultsView/mutation/MutationMapper.tsx
@@ -78,13 +78,14 @@ export default class MutationMapper extends React.Component<IMutationMapperProps
             <div style={{'paddingBottom':10}}>
                 <h4>{hugoGeneSymbol}</h4>
                 <div className={this.props.store.uniprotId.result ? '' : 'invisible'}>
-                    <span data-test="GeneSummaryUniProt">UniProt: </span>
-                    <a
-                        href={`http://www.uniprot.org/uniprot/${uniprotId}`}
-                        target="_blank"
-                    >
-                        {uniprotId}
-                    </a>
+                    <span data-test="GeneSummaryUniProt">{'UniProt: '}
+                        <a
+                            href={`http://www.uniprot.org/uniprot/${uniprotId}`}
+                            target="_blank"
+                        >
+                            {uniprotId}
+                        </a>
+                    </span>
                 </div>
                 <div className={this.props.store.canonicalTranscript.result ? '' : 'invisible'}>
                     <span>Transcript: </span>

diff --git a/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.spec.tsx b/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.spec.tsx
@@ -26,6 +26,18 @@ const exampleData = [
         "adjustedPValue": 0.023809523809523704,
         "association": "Mutual exclusivity"
     },
+    {
+        "geneA": "TP53",
+        "geneB": "BRAF",
+        "neitherCount": 6,
+        "aNotBCount": 0,
+        "bNotACount": 1,
+        "bothCount": 3,
+        "logOddsRatio": Infinity,
+        "pValue": 0.03333333333333314,
+        "adjustedPValue": 0.19999999999999885,
+        "association": "Co-occurrence"
+    },
     {
         "geneA": "EGFR",
         "geneB": "TP53",
@@ -73,18 +85,6 @@ const exampleData = [
         "pValue": 0.2619047619047609,
         "adjustedPValue": 1,
         "association": "Co-occurrence"
-    },
-    {
-        "geneA": "TP53",
-        "geneB": "BRAF",
-        "neitherCount": 6,
-        "aNotBCount": 0,
-        "bNotACount": 1,
-        "bothCount": 3,
-        "logOddsRatio": Infinity,
-        "pValue": 0.03333333333333314,
-        "adjustedPValue": 0.19999999999999885,
-        "association": "Co-occurrence"
     }
 ];
 
@@ -242,8 +242,8 @@ describe("MutualExclusivityUtil", () => {
                         "bNotACount": 5,
                         "bothCount": 0,
                         "logOddsRatio": -6.51,
-                        "pValue": 0.04,
-                        "adjustedPValue": 0.08,
+                        "pValue": 0.02,
+                        "adjustedPValue": 0.04,
                         "association": "Mutual exclusivity"
                     },
                     {
@@ -277,8 +277,8 @@ describe("MutualExclusivityUtil", () => {
                     "bNotACount": 5,
                     "bothCount": 0,
                     "logOddsRatio": -6.51,
-                    "pValue": 0.04,
-                    "adjustedPValue": 0.08,
+                    "pValue": 0.02,
+                    "adjustedPValue": 0.04,
                     "association": "Mutual exclusivity"
                 },
                 {

diff --git a/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.tsx b/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.tsx
@@ -3,6 +3,7 @@ import { getCumulativePValue } from "../../../shared/lib/FisherExactTestCalculat
 import { MutualExclusivity } from "../../../shared/model/MutualExclusivity";
 import Combinatorics from 'js-combinatorics';
 import Dictionary = _.Dictionary;
+import * as _ from 'lodash';
 
 export function calculateAssociation(logOddsRatio: number): string {
     return logOddsRatio > 0 ? "Co-occurrence" : "Mutual exclusivity";
@@ -55,7 +56,7 @@ export function getMutuallyExclusiveCounts(data: MutualExclusivity[],
     let significantCount = null;
 
     const exclusiveData = data.filter(mutualExclusivity => exclusive(mutualExclusivity.logOddsRatio));
-    const significantData = exclusiveData.filter(mutualExclusivity => mutualExclusivity.pValue < 0.05);
+    const significantData = exclusiveData.filter(mutualExclusivity => mutualExclusivity.adjustedPValue < 0.05);
 
     const exclusiveLength = exclusiveData.length;
     const significantLength = significantData.length;
@@ -105,7 +106,7 @@ export function getData(isSampleAlteredMap: Dictionary<boolean[]>): MutualExclus
             bothCount: counts[3], logOddsRatio, pValue, 
             adjustedPValue: calculateAdjustedPValue(pValue, combinations.length), association });
     });
-    return data;
+    return _.sortBy(data, ["pValue"]);
 }
 
 export function getFilteredData(data: MutualExclusivity[], mutualExclusivityFilter: boolean, coOccurenceFilter: boolean,
@@ -120,7 +121,7 @@ export function getFilteredData(data: MutualExclusivity[], mutualExclusivityFilt
             result = result || mutualExclusivity.logOddsRatio > 0;
         }
         if (significantPairsFilter) {
-            result = result && mutualExclusivity.pValue < 0.05;
+            result = result && mutualExclusivity.adjustedPValue < 0.05;
         }
         return result;
     });