@vitessce/statistical-plots 3.5.9 → 3.5.11

package/src/utils.js

@@ -1,9 +1,9 @@
+/* eslint-disable camelcase */
 import { useMemo } from 'react';
 import { isEqual } from 'lodash-es';
 import { colorArrayToString } from '@vitessce/sets-utils';
 import { getDefaultColor } from '@vitessce/utils';
 
-
 function createOrdinalScale(domainArr, rangeArr) {
   return (queryVal) => {
     const i = domainArr.findIndex(domainVal => isEqual(domainVal, queryVal));
@@ -45,3 +45,84 @@ export function useRawSetPaths(columnNameMapping, setPaths) {
     return newSetPath;
   }), [columnNameMapping, setPaths]);
 }
+
+// Data transformation hook function that is used both here
+// and in the FeatureStatsTable view.
+export function useFilteredVolcanoData(props) {
+  const {
+    data,
+    obsSetsColumnNameMappingReversed,
+    sampleSetsColumnNameMappingReversed,
+    featurePointFoldChangeThreshold,
+    featurePointSignificanceThreshold,
+    sampleSetSelection,
+  } = props;
+
+
+  const computedData = useMemo(() => data.map((d) => {
+    const { metadata } = d;
+
+    const coordinationValues = metadata.coordination_values;
+
+    const rawObsSetPath = coordinationValues.obsSetFilter
+      ? coordinationValues.obsSetFilter[0]
+      : coordinationValues.obsSetSelection[0];
+    const obsSetPath = [...rawObsSetPath];
+    obsSetPath[0] = obsSetsColumnNameMappingReversed[rawObsSetPath[0]];
+
+    // Swap the foldchange direction if backwards with
+    // respect to the current sampleSetSelection pair.
+    // TODO: move this swapping into the computedData useMemo?
+    let shouldSwapFoldChangeDirection = false;
+    if (
+      coordinationValues.sampleSetFilter
+      && coordinationValues.sampleSetFilter.length === 2
+    ) {
+      const rawSampleSetPathA = coordinationValues.sampleSetFilter[0];
+      const sampleSetPathA = [...rawSampleSetPathA];
+      sampleSetPathA[0] = sampleSetsColumnNameMappingReversed[rawSampleSetPathA[0]];
+
+      const rawSampleSetPathB = coordinationValues.sampleSetFilter[1];
+      const sampleSetPathB = [...rawSampleSetPathB];
+      sampleSetPathB[0] = sampleSetsColumnNameMappingReversed[rawSampleSetPathB[0]];
+
+      if (
+        isEqual(sampleSetPathA, sampleSetSelection[1])
+        && isEqual(sampleSetPathB, sampleSetSelection[0])
+      ) {
+        shouldSwapFoldChangeDirection = true;
+      }
+    }
+
+    return ({
+      ...d,
+      df: {
+        ...d.df,
+        minusLog10p: d.df.featureSignificance.map(v => -Math.log10(v)),
+        logFoldChange: d.df.featureFoldChange.map(v => (
+          Math.log2(v) * (shouldSwapFoldChangeDirection ? -1 : 1)
+        )),
+      },
+    });
+  }), [
+    data, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMappingReversed,
+    sampleSetSelection,
+  ]);
+
+  const filteredData = useMemo(() => computedData.map(obj => ({
+    ...obj,
+    // Instead of an object of one array per column,
+    // this is now an array of one object per row.
+    df: obj.df.featureId.map((featureId, i) => ({
+      featureId,
+      logFoldChange: obj.df.logFoldChange[i],
+      featureSignificance: obj.df.featureSignificance[i],
+      minusLog10p: obj.df.minusLog10p[i],
+    })).filter(d => (
+      (Math.abs(d.logFoldChange) >= (featurePointFoldChangeThreshold ?? 1.0))
+      && (d.featureSignificance <= (featurePointSignificanceThreshold ?? 0.05))
+    )),
+  })), [computedData, featurePointFoldChangeThreshold, featurePointSignificanceThreshold]);
+
+  return [computedData, filteredData];
+}