added co-occurrence patern, p value, q value, enriched in columns and…

… dropdown, shift click message. specified fisher test use in text
cBioPortal · Apr 10, 2023 · 600a1de · 600a1de
1 parent 5abb62d
commit 600a1de
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Showing 20 changed files with 896 additions and 442 deletions.
diff --git a/packages/react-mutation-mapper/src/component/lollipopMutationPlot/PercentToggle.tsx b/packages/react-mutation-mapper/src/component/lollipopMutationPlot/PercentToggle.tsx
@@ -26,7 +26,6 @@ export class PercentToggle extends React.Component<IPercentToggleProps, {}> {
                 <div
                     style={{
                         marginLeft: 10,
-                        marginRight: 10,
                     }}
                 >
                     <div style={{ textAlign: 'center' }}>Y-Axis:</div>

diff --git a/packages/react-mutation-mapper/src/component/mutationMapper/FilterResetPanel.tsx b/packages/react-mutation-mapper/src/component/mutationMapper/FilterResetPanel.tsx
@@ -7,6 +7,7 @@ import styles from './filterResetPanel.module.scss';
 type FilterResetPanelProps = {
     resetFilters: () => void;
     filterInfo?: JSX.Element | string;
+    shiftClickMessage?: JSX.Element | string;
     className?: string;
     buttonText?: string;
     buttonClass?: string;
@@ -42,6 +43,7 @@ export class FilterResetPanel extends React.Component<
                     >
                         {this.props.buttonText}
                     </button>
+                    {this.props.shiftClickMessage}
                 </span>
             </div>
         );

diff --git a/src/pages/groupComparison/FisherExactTwoSidedTestLabel.tsx b/src/pages/groupComparison/FisherExactTwoSidedTestLabel.tsx
@@ -2,111 +2,71 @@ import { action, makeObservable, observable } from 'mobx';
 import { observer } from 'mobx-react';
 import * as React from 'react';
 import MutationMapperDataStore from 'shared/components/mutationMapper/MutationMapperDataStore';
-import { ComparisonGroup, getSampleIdentifiers } from './GroupComparisonUtils';
+import {
+    ComparisonGroup,
+    getPatientIdentifiers,
+    getSampleIdentifiers,
+} from './GroupComparisonUtils';
 import { toConditionalPrecisionWithMinimum } from 'shared/lib/FormatUtils';
 import _ from 'lodash';
+import { getTwoTailedPValue } from 'shared/lib/FisherExactTestCalculator';
+import ComplexKeyMap from 'shared/lib/complexKeyDataStructures/ComplexKeyMap';
+import { Sample } from 'cbioportal-ts-api-client';
+import { countUniqueMutations } from 'shared/lib/MutationUtils';
 
 interface IFisherExactTwoSidedTestLabelProps {
     dataStore: MutationMapperDataStore;
     groups: ComparisonGroup[];
-    maxSize: number;
+    sampleSet: ComplexKeyMap<Sample>;
 }
 
 export const FisherExactTwoSidedTestLabel: React.FC<IFisherExactTwoSidedTestLabelProps> = observer(
-    ({ dataStore, groups, maxSize }: IFisherExactTwoSidedTestLabelProps) => {
-        // initialize array of factorials for speed
-        let f = new Array(maxSize + 1);
-        f[0] = 0.0;
-        for (let i = 1; i <= maxSize; i++) {
-            f[i] = f[i - 1] + Math.log(i);
-        }
-
-        const mutationCountForActiveGeneGroupA = _.intersection(
-            _.flatten(dataStore.tableData),
-            _.flatten(dataStore.sortedFilteredGroupedData[0].data)
-        ).length;
-        const mutationCountForActiveGeneGroupB = _.intersection(
-            _.flatten(dataStore.tableData),
-            _.flatten(dataStore.sortedFilteredGroupedData[1].data)
-        ).length;
-        const sampleCountForGroupA = getSampleIdentifiers([groups[0]]).length;
-        const sampleCountForGroupB = getSampleIdentifiers([groups[1]]).length;
-
-        const getP = (a: number, b: number, c: number, d: number): number => {
-            let n = a + b + c + d;
-            if (n > maxSize) {
-                return NaN;
-            }
-            let p;
-            p =
-                f[a + b] +
-                f[c + d] +
-                f[a + c] +
-                f[b + d] -
-                (f[a] + f[b] + f[c] + f[d] + f[n]);
-            return Math.exp(p);
-        };
-
-        const getTwoTailedP = (
-            a: number,
-            b: number,
-            c: number,
-            d: number
-        ): number => {
-            let min, i;
-            let n = a + b + c + d;
-            if (n > maxSize) {
-                return NaN;
-            }
-            let p = 0;
-
-            let baseP = getP(a, b, c, d);
-            // in order for a table under consideration to have its p-value included
-            // in the final result, it must have a p-value less than the baseP, i.e.
-            // Fisher's exact test computes the probability, given the observed marginal
-            // frequencies, of obtaining exactly the frequencies observed and any configuration more extreme.
-            // By "more extreme," we mean any configuration (given observed marginals) with a smaller probability of
-            // occurrence in the same direction (one-tailed) or in both directions (two-tailed).
-
-            let initialA = a,
-                initialB = b,
-                initialC = c,
-                initialD = d;
-            p += baseP;
-
-            min = c < b ? c : b;
-            for (i = 0; i < min; i++) {
-                let tempP = getP(++a, --b, --c, ++d);
-                if (tempP <= baseP) {
-                    p += tempP;
-                }
-            }
-
-            // reset the values to their original so we can repeat this process for the other side
-            a = initialA;
-            b = initialB;
-            c = initialC;
-            d = initialD;
+    ({ dataStore, groups, sampleSet }: IFisherExactTwoSidedTestLabelProps) => {
+        const mutationCountForActiveGeneGroupA = countUniqueMutations(
+            _.intersection(
+                _.flatten(dataStore.tableData),
+                _.flatten(dataStore.sortedFilteredGroupedData[0].data)
+            )
+        );
+        const mutationCountForActiveGeneGroupB = countUniqueMutations(
+            _.intersection(
+                _.flatten(dataStore.tableData),
+                _.flatten(dataStore.sortedFilteredGroupedData[1].data)
+            )
+        );
+        const sampleIdentifiersForGroupA = getSampleIdentifiers([groups[0]]);
+        const patientIdentifiersforGroupA = getPatientIdentifiers(
+            sampleIdentifiersForGroupA,
+            sampleSet
+        );
+        const sampleIdentifiersForGroupB = getSampleIdentifiers([groups[1]]);
+        const patientIdentifiersforGroupB = getPatientIdentifiers(
+            sampleIdentifiersForGroupB,
+            sampleSet
+        );
 
-            min = a < d ? a : d;
-            for (i = 0; i < min; i++) {
-                let pTemp = getP(--a, ++b, ++c, --d);
-                if (pTemp <= baseP) {
-                    p += pTemp;
-                }
+        const getFisherTestLabel = () => {
+            if (dataStore.sortedFilteredSelectedData.length > 0) {
+                return 'Fisher Exact Two-Sided Test p-value for selected mutations: ';
+            } else if (
+                dataStore.sortedFilteredData.length < dataStore.allData.length
+            ) {
+                return 'Fisher Exact Two-Sided Test p-value for filtered mutations: ';
             }
-            return p;
+            return 'Fisher Exact Two-Sided Test p-value for all mutations: ';
         };
 
         return (
             <div style={{ fontWeight: 'bold' }}>
-                Fisher Exact Two-Sided Test p-value:{' '}
+                {getFisherTestLabel()}
                 {toConditionalPrecisionWithMinimum(
-                    getTwoTailedP(
+                    getTwoTailedPValue(
                         mutationCountForActiveGeneGroupA,
-                        sampleCountForGroupA - mutationCountForActiveGeneGroupA,
+                        patientIdentifiersforGroupA.length -
+                            mutationCountForActiveGeneGroupA,
                         mutationCountForActiveGeneGroupB,
-                        sampleCountForGroupB - mutationCountForActiveGeneGroupB
+                        patientIdentifiersforGroupB.length -
+                            mutationCountForActiveGeneGroupB
                     ),
                     3,
                     0.01,