diff --git a/src/pages/resultsView/mutation/MutationMapper.tsx b/src/pages/resultsView/mutation/MutationMapper.tsx index 95c35958c1c..9f67e4131f7 100644 --- 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

{hugoGeneSymbol}

- UniProt: - - {uniprotId} - + {'UniProt: '} + + {uniprotId} + +
Transcript: diff --git a/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.spec.tsx b/src/pages/resultsView/mutualExclusivity/MutualExclusivityUtil.spec.tsx index 15489b829f6..bb0ba1b973d 100644 --- 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 index 47c5b5ba6f4..dafbf5123ee 100644 --- 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): 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; });