spatialquery.js 0.0.0-stage → 0.1.1

package/dist/nested.js

@@ -0,0 +1,106 @@
+import { applyFdrCorrection } from './stats.js';
+import { findMaximalPatterns } from './fpgrowth.js';
+// Nested motif testing.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_utils.py#L97
+//
+// The maximal-pattern reduction happens BEFORE the hypergeometric test, so a sub-pattern
+// of a non-significant maximal pattern never enters the tested set at all. When a maximal
+// pattern is diluted by one abundant, unrelated cell type, the whole pattern fails the
+// test and the informative core inside it is never examined.
+//
+// Nested testing walks into those patterns:
+//
+//   1. Test every maximal pattern, exactly as the maximal mode does.
+//   2. A maximal pattern that IS significant is a finding in its own right -- stop, and do
+//      not test its sub-patterns.
+//   3. A maximal pattern that is NOT significant is expanded into its immediate (k-1)
+//      sub-patterns, which are then tested.
+//   4. Descent continues only along branches that stay non-significant. A branch ends when
+//      it becomes significant or reaches length 1.
+//   5. A sub-pattern reachable from several parents is tested once.
+//   6. Multiple-testing correction is applied over every pattern actually tested.
+//   7. A child whose support equals its parent's marks the same neighborhoods as the
+//      parent, so it carries no extra information and is not reported.
+const NESTED_SUPPORT_TOL = 1e-9;
+const NESTED_MAX_TESTED_PATTERNS = 5000;
+const NESTED_MAX_EXPANSION_FACTOR = 50.0;
+// Canonical motif key: the sorted motif.
+const canonicalKey = (motif) => JSON.stringify(motif.toSorted());
+// Run the nested descent and return the corrected results over everything tested.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_utils.py#L161
+export async function nestedMotifDescent(params) {
+    const { testMotifs, frequentPatterns, supportTol = NESTED_SUPPORT_TOL, maxTestedPatterns = NESTED_MAX_TESTED_PATTERNS, maxExpansionFactor = NESTED_MAX_EXPANSION_FACTOR, } = params;
+    if (frequentPatterns.length === 0) {
+        return [];
+    }
+    const supportOf = new Map(frequentPatterns.map(p => [canonicalKey(p.itemsets), p.support]));
+    const maximal = findMaximalPatterns(frequentPatterns).map(p => p.itemsets.toSorted());
+    // Level 0 is the maximal patterns; gating them decides where the descent starts.
+    const gateRes = maximal.length > 0 ? await testMotifs(maximal) : [];
+    if (gateRes.length === 0) {
+        return [];
+    }
+    const significance = (results) => new Map(results.map(r => [canonicalKey(r.motifs), Boolean(r.ifSignificant)]));
+    const gateSig = significance(gateRes);
+    // `tested` records every pattern the descent touches, significant or not: correction
+    // in rule 6 must cover them all. Insertion order keeps the final results reproducible.
+    const tested = new Set(maximal.map(canonicalKey));
+    const parentOf = new Map();
+    const levelTables = [gateRes];
+    let frontier = maximal.filter(m => !gateSig.get(canonicalKey(m)));
+    while (frontier.length > 0) {
+        const children = [];
+        for (const parent of frontier) {
+            if (parent.length <= 1)
+                continue;
+            // Immediate sub-patterns, in the order of itertools.combinations(parent, len(parent) - 1).
+            for (let drop = parent.length - 1; drop >= 0; drop--) {
+                const child = parent.filter((_, n) => n !== drop);
+                const childKey = canonicalKey(child);
+                if (tested.has(childKey)) {
+                    // Reachable from an earlier parent already: test it once, and keep the
+                    // shallowest parent, which breadth-first order guarantees is this one.
+                    continue;
+                }
+                tested.add(childKey);
+                parentOf.set(childKey, canonicalKey(parent));
+                children.push(child);
+            }
+        }
+        if (children.length === 0)
+            break;
+        if (tested.size > maxTestedPatterns || tested.size > maxExpansionFactor * Math.max(maximal.length, 1)) {
+            console.warn(`Nested descent stopped early at ${tested.size} tested patterns `
+                + `(limits: maxTestedPatterns=${maxTestedPatterns}, `
+                + `maxExpansionFactor=${maxExpansionFactor} x ${maximal.length} maximal patterns). `
+                + `Reported results cover the patterns reached so far.`);
+            break;
+        }
+        const levelRes = await testMotifs(children);
+        levelTables.push(levelRes);
+        const levelSig = significance(levelRes);
+        frontier = children.filter(c => !levelSig.get(canonicalKey(c)));
+    }
+    // Every field except the FDR ones depends only on the motif and the data, so the
+    // results computed level by level are reused; only the correction is redone over the union.
+    const seen = new Set();
+    const combined = levelTables.flat().filter((r) => {
+        const key = canonicalKey(r.motifs);
+        if (seen.has(key))
+            return false;
+        seen.add(key);
+        return true;
+    });
+    // Rule 7: a child marking the same neighborhoods as its parent adds nothing. It stays
+    // in the correction -- it was tested -- but is not reported.
+    const redundant = new Set();
+    for (const [child, parent] of parentOf) {
+        const supportChild = supportOf.get(child);
+        const supportParent = supportOf.get(parent);
+        if (supportChild !== undefined && supportParent !== undefined && Math.abs(supportChild - supportParent) <= supportTol) {
+            redundant.add(child);
+        }
+    }
+    return applyFdrCorrection(combined).filter(r => !redundant.has(canonicalKey(r.motifs)));
+}
+//# sourceMappingURL=nested.js.map

package/dist/nested.js.map

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package/dist/single-fov.d.ts

@@ -0,0 +1,149 @@
+import Flatbush from 'flatbush';
+import { type FrequentPattern } from './fpgrowth.js';
+export declare function generateObsIdToObsSetName(obsSetsMembership: Map<string, string[][]>, currSelectedSetGroup: string): (obsId: string) => string;
+type ToObsSetNameFunc = ReturnType<typeof generateObsIdToObsSetName>;
+type Coords = Float32Array | Float64Array;
+export type InitParams = {
+    obsIndex: string[];
+    xCoords: Coords;
+    yCoords: Coords;
+    obsIdToObsSetName: ToObsSetNameFunc;
+    leafSize?: number;
+    normalizeSpatialCoord?: boolean;
+};
+export type SqContext = {
+    obsIndex: string[];
+    labels: string[];
+    xCoords: Coords;
+    yCoords: Coords;
+    flatbushIndex: Flatbush;
+    xExtent: [number, number];
+    yExtent: [number, number];
+};
+export declare function normalizeSpatialCoords(xCoords: Coords, yCoords: Coords): {
+    xCoords: Float64Array<ArrayBuffer>;
+    yCoords: Float64Array<ArrayBuffer>;
+    scaleFactor: number;
+};
+export declare function buildContext(params: InitParams): SqContext;
+export declare function findCellIndicesOfType(context: SqContext, ct: string): number[];
+export type QueryPoint = {
+    x: number;
+    y: number;
+    exclude?: number;
+};
+export declare function knnNeighborhood(context: SqContext, k: number, maxDist: number): (i: number) => number[];
+export declare function radiusNeighborhood(context: SqContext, maxDist: number): (i: number) => number[];
+export declare function radiusTransactions(context: SqContext, points: QueryPoint[], maxDist: number, minSize: number): {
+    transactions: string[][];
+    neighborLists: number[][];
+};
+export declare function knnTransactions(context: SqContext, cinds: number[], k: number, maxDist: number): string[][];
+type FindPatternsParams = {
+    maxDist?: number;
+    minSize?: number;
+    minSupport?: number;
+    returnCellIds?: boolean;
+};
+export declare function buildGridPoints(context: SqContext, maxDist?: number): [number, number][];
+export declare function findPatternsGrid(context: SqContext, params?: FindPatternsParams): Promise<FrequentPattern[]>;
+export declare function findPatternsRand(context: SqContext, params?: FindPatternsParams & {
+    nPoints?: number;
+}): Promise<FrequentPattern[]>;
+type FindFpKnnParams = {
+    ct: string;
+    k?: number;
+    minSupport?: number;
+    maxDist?: number;
+    ifMax?: boolean;
+};
+export declare function findFpKnn(context: SqContext, params: FindFpKnnParams): Promise<FrequentPattern[]>;
+type FindFpDistParams = {
+    ct: string;
+    maxDist?: number;
+    minSize?: number;
+    minSupport?: number;
+    ifMax?: boolean;
+};
+export declare function findFpDist(context: SqContext, params: FindFpDistParams): Promise<FrequentPattern[]>;
+export declare function centerQueryPoints(context: SqContext, cinds: number[]): QueryPoint[];
+type MotifEnrichmentCountsParams = {
+    center: string;
+    motif: string[];
+    numCells: number;
+    numCenter: number;
+    numMotif: number;
+    numCenterMotif: number;
+};
+export type MotifEnrichmentResult = {
+    center: string;
+    motifs: string[];
+    nCenterMotif: number;
+    nCenter: number;
+    nMotif: number;
+    expectation: number;
+    pValue: number;
+    ifSignificant?: boolean;
+    adjPValue?: number;
+    neighborIds?: string[];
+    centerIds?: string[];
+};
+export declare function computeMotifEnrichment(params: MotifEnrichmentCountsParams): MotifEnrichmentResult;
+export type MotifsParam = string | string[] | string[][];
+export declare function normalizeMotifs(motifs: MotifsParam, labelsUnique: Set<string>): string[][];
+export declare function normalizeMotifList(motifs: MotifsParam, labelsUnique: Set<string>): string[][];
+export type MotifCounts = {
+    numCells: number;
+    numCenter: number;
+    numMotif: number;
+    numCenterMotif: number;
+    centerIndices?: number[];
+    neighborIndices?: number[];
+};
+export declare function countMotifs(context: SqContext, ct: string, motifs: string[][], neighborsOf: (i: number) => number[], returnCellIds: boolean): MotifCounts[];
+export type EnrichmentMode = 'maximal' | 'nested';
+export declare function assertEnrichmentMode(mode: string): void;
+type MotifEnrichmentKnnParams = {
+    ct: string;
+    motifs?: MotifsParam;
+    k?: number;
+    minSupport?: number;
+    maxDist?: number;
+    returnCellIds?: boolean;
+    mode?: EnrichmentMode;
+};
+export declare function motifEnrichmentKnn(context: SqContext, params: MotifEnrichmentKnnParams): Promise<MotifEnrichmentResult[]>;
+type MotifEnrichmentDistParams = {
+    ct: string;
+    motifs?: MotifsParam;
+    maxDist?: number;
+    minSize?: number;
+    minSupport?: number;
+    returnCellIds?: boolean;
+    mode?: EnrichmentMode;
+};
+export declare function motifEnrichmentDist(context: SqContext, params: MotifEnrichmentDistParams): Promise<MotifEnrichmentResult[]>;
+export type MotifCompositionRow = {
+    center: string;
+    motifs: string[];
+    cellType: string;
+    nCells: number;
+    nMotifCells: number;
+    proportion: number;
+};
+export declare function motifCompositionRows(context: SqContext, ct: string, motifs: string[][], cinds: number[], neighborsOf: (i: number) => number[]): MotifCompositionRow[];
+type MotifCompositionKnnParams = {
+    ct: string;
+    motifs: MotifsParam;
+    k?: number;
+    maxDist?: number;
+};
+export declare function motifCompositionKnn(context: SqContext, params: MotifCompositionKnnParams): MotifCompositionRow[];
+type MotifCompositionDistParams = {
+    ct: string;
+    motifs: MotifsParam;
+    maxDist?: number;
+};
+export declare function motifCompositionDist(context: SqContext, params: MotifCompositionDistParams): MotifCompositionRow[];
+export {};
+//# sourceMappingURL=single-fov.d.ts.map

package/dist/single-fov.d.ts.map

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