spatialquery.js 0.0.0-stage → 0.1.0

package/dist/multi-fov.js

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+// Port of the multi-FOV class spatial_query_multi.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py
+import { buildContext, findCellIndicesOfType, knnTransactions, radiusTransactions, centerQueryPoints, knnNeighborhood, radiusNeighborhood, countMotifs, computeMotifEnrichment, normalizeMotifs, normalizeMotifList, motifCompositionRows, assertEnrichmentMode, findFpKnn as findFpKnnSingle, findFpDist as findFpDistSingle, } from './single-fov.js';
+import { mineFrequentPatterns } from './fpgrowth.js';
+import { nestedMotifDescent } from './nested.js';
+import { applyFdrCorrection, fdrCorrection, mannWhitneyU, rankAverage, median, mean } from './stats.js';
+// Build the multi-FOV context object.
+// Unlike Python, which derives unique FOV names from the (possibly repeated) dataset names
+// ('name' -> 'name_0', 'name_1', ...), each FOV has an explicit ID and class.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L43
+export function buildMultiContext(fovs) {
+    const datasetIds = fovs.map(fov => fov.datasetId);
+    const duplicates = datasetIds.filter((id, i) => datasetIds.indexOf(id) !== i);
+    if (duplicates.length > 0) {
+        throw new Error(`Dataset IDs must be unique. Found duplicates: ${Array.from(new Set(duplicates)).join(', ')}`);
+    }
+    return {
+        datasetIds,
+        datasetClasses: fovs.map(fov => fov.datasetClass),
+        contexts: fovs.map(fov => buildContext(fov)),
+    };
+}
+// The datasets (FOVs) belonging to the selected classes (all classes if not provided).
+function selectFovs(multi, datasetClass) {
+    const validClasses = new Set(multi.datasetClasses);
+    const selected = datasetClass === undefined
+        ? validClasses
+        : new Set(typeof datasetClass === 'string' ? [datasetClass] : datasetClass);
+    for (const c of selected) {
+        if (!validClasses.has(c)) {
+            throw new Error(`Invalid dataset class: ${c}. Valid dataset classes are: ${Array.from(validClasses).join(', ')}`);
+        }
+    }
+    return multi.contexts
+        .map((context, i) => ({ datasetId: multi.datasetIds[i], datasetClass: multi.datasetClasses[i], context }))
+        .filter(fov => selected.has(fov.datasetClass));
+}
+// Throws if the cell type is absent from every FOV (selected or not, as in Python).
+function assertCellTypeInAnyFov(multi, ct) {
+    if (!multi.contexts.some(context => context.labels.includes(ct))) {
+        throw new Error(`Found no ${ct} in any datasets!`);
+    }
+}
+// Unique cell type labels across all FOVs.
+function allLabels(multi) {
+    return new Set(multi.contexts.flatMap(context => context.labels));
+}
+// Find frequent patterns within the k-NN neighborhoods of a cell type, pooling the
+// neighborhoods of all selected FOVs.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L116
+export async function multiFindFpKnn(multi, params) {
+    const { ct, datasetClass, k = 30, minSupport = 0.5, maxDist = 20, ifMax = true } = params;
+    assertCellTypeInAnyFov(multi, ct);
+    const transactions = selectFovs(multi, datasetClass).flatMap(({ context }) => (knnTransactions(context, findCellIndicesOfType(context, ct), k, maxDist)));
+    return mineFrequentPatterns(transactions, minSupport, ifMax);
+}
+// Find frequent patterns within the radius-based neighborhoods of a cell type, pooling the
+// neighborhoods of all selected FOVs.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L219
+export async function multiFindFpDist(multi, params) {
+    const { ct, datasetClass, maxDist = 20, minSize = 0, minSupport = 0.5, ifMax = true } = params;
+    assertCellTypeInAnyFov(multi, ct);
+    const transactions = selectFovs(multi, datasetClass).flatMap(({ context }) => {
+        const points = centerQueryPoints(context, findCellIndicesOfType(context, ct));
+        return radiusTransactions(context, points, maxDist, minSize).transactions;
+    });
+    return mineFrequentPatterns(transactions, minSupport, ifMax);
+}
+function getFov(multi, datasetId) {
+    const index = multi.datasetIds.indexOf(datasetId);
+    if (index === -1) {
+        throw new Error(`Found no dataset with ID ${datasetId}.`);
+    }
+    return multi.contexts[index];
+}
+// Find frequent (maximal) patterns within the k-NN neighborhoods of a cell type in a single FOV.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L993
+export async function findFpKnnFov(multi, params) {
+    const { ct, datasetId, k = 30, minSupport = 0.5, maxDist = 20 } = params;
+    const context = getFov(multi, datasetId);
+    if (!context.labels.includes(ct))
+        return [];
+    return findFpKnnSingle(context, { ct, k, minSupport, maxDist });
+}
+// Find frequent (maximal) patterns within the radius-based neighborhoods of a cell type in a single FOV.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L1049
+export async function findFpDistFov(multi, params) {
+    const { ct, datasetId, maxDist = 20, minSize = 0, minSupport = 0.5 } = params;
+    const context = getFov(multi, datasetId);
+    if (!context.labels.includes(ct))
+        return [];
+    return findFpDistSingle(context, { ct, maxDist, minSize, minSupport });
+}
+// Normalize user-specified motifs against the labels of all FOVs, throwing if none remain.
+function normalizeMultiMotifs(multi, motifs) {
+    const filtered = normalizeMotifs(motifs, allLabels(multi));
+    if (filtered.length === 0) {
+        throw new Error("All cell types in motifs are missing in the cell type labels.");
+    }
+    return filtered;
+}
+function multiMotifEnrichment(fovs, ct, motifs, neighborhood, returnCellIds) {
+    const totals = motifs.map(() => ({ numCells: 0, numCenter: 0, numMotif: 0, numCenterMotif: 0 }));
+    const neighborIds = motifs.map(() => ({}));
+    const centerIds = motifs.map(() => ({}));
+    for (const { datasetId, context } of fovs) {
+        const counts = countMotifs(context, ct, motifs, neighborhood(context), returnCellIds);
+        counts.forEach((c, m) => {
+            totals[m].numCells += c.numCells;
+            totals[m].numCenter += c.numCenter;
+            totals[m].numMotif += c.numMotif;
+            totals[m].numCenterMotif += c.numCenterMotif;
+            if (returnCellIds && c.centerIndices.length > 0) {
+                neighborIds[m][datasetId] = c.neighborIndices.map(j => context.obsIndex[j]);
+                centerIds[m][datasetId] = c.centerIndices.map(i => context.obsIndex[i]);
+            }
+        });
+    }
+    const out = motifs.map((motif, m) => {
+        const { neighborIds: _n, centerIds: _c, ...result } = computeMotifEnrichment({ center: ct, motif, ...totals[m] });
+        return returnCellIds
+            ? { ...result, neighborIds: neighborIds[m], centerIds: centerIds[m] }
+            : result;
+    });
+    return applyFdrCorrection(out);
+}
+// Perform motif enrichment analysis using k-nearest neighbors in multiple FOVs.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L319
+export async function multiMotifEnrichmentKnn(multi, params) {
+    const { ct, datasetClass, k = 30, minSupport = 0.5, maxDist = 20, returnCellIds = false, mode = 'maximal' } = params;
+    const fovs = selectFovs(multi, datasetClass);
+    assertCellTypeInAnyFov(multi, ct);
+    assertEnrichmentMode(mode);
+    if (mode === 'nested' && params.motifs === undefined) {
+        return nestedMotifDescent({
+            testMotifs: motifs => multiMotifEnrichmentKnn(multi, { ...params, motifs, mode: 'maximal' }),
+            frequentPatterns: await multiFindFpKnn(multi, { ct, datasetClass, k, minSupport, maxDist, ifMax: false }),
+        });
+    }
+    const motifs = params.motifs === undefined
+        ? (await multiFindFpKnn(multi, { ct, datasetClass, k, minSupport, maxDist })).map(p => p.itemsets)
+        : normalizeMultiMotifs(multi, params.motifs);
+    return multiMotifEnrichment(fovs, ct, motifs, context => knnNeighborhood(context, k, maxDist), returnCellIds);
+}
+// Perform motif enrichment analysis within a radius-based neighborhood in multiple FOVs.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L581
+export async function multiMotifEnrichmentDist(multi, params) {
+    const { ct, datasetClass, maxDist = 20, minSize = 0, minSupport = 0.5, returnCellIds = false, mode = 'maximal' } = params;
+    const fovs = selectFovs(multi, datasetClass);
+    assertCellTypeInAnyFov(multi, ct);
+    assertEnrichmentMode(mode);
+    if (mode === 'nested' && params.motifs === undefined) {
+        return nestedMotifDescent({
+            testMotifs: motifs => multiMotifEnrichmentDist(multi, { ...params, motifs, mode: 'maximal' }),
+            frequentPatterns: await multiFindFpDist(multi, { ct, datasetClass, maxDist, minSize, minSupport, ifMax: false }),
+        });
+    }
+    const motifs = params.motifs === undefined
+        ? (await multiFindFpDist(multi, { ct, datasetClass, maxDist, minSize, minSupport })).map(p => p.itemsets)
+        : normalizeMultiMotifs(multi, params.motifs);
+    return multiMotifEnrichment(fovs, ct, motifs, context => radiusNeighborhood(context, maxDist), returnCellIds);
+}
+// Pool the motif composition over the selected FOVs.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L851
+function multiMotifComposition(multi, ct, motifsParam, datasetClass, neighborhood) {
+    const fovs = selectFovs(multi, datasetClass);
+    assertCellTypeInAnyFov(multi, ct);
+    const motifs = normalizeMotifList(motifsParam, allLabels(multi));
+    return fovs.flatMap(({ datasetId, context }) => {
+        const cinds = findCellIndicesOfType(context, ct);
+        const labelsUnique = new Set(context.labels);
+        // A motif with a cell type missing from this FOV has no motif-positive center here.
+        const active = motifs.filter(m => m.every(t => labelsUnique.has(t)));
+        if (cinds.length === 0 || active.length === 0)
+            return [];
+        return motifCompositionRows(context, ct, active, cinds, neighborhood(context))
+            .map(row => ({ datasetId, ...row }));
+    });
+}
+// Compute the composition of motif cell types in the k-NN neighborhoods of center cells across multiple FOVs.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L931
+export function multiMotifCompositionKnn(multi, params) {
+    const { ct, motifs, datasetClass, k = 30, maxDist = 20 } = params;
+    return multiMotifComposition(multi, ct, motifs, datasetClass, context => knnNeighborhood(context, k, maxDist));
+}
+// Compute the composition of motif cell types in the radius-based neighborhoods of center cells across multiple FOVs.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L888
+export function multiMotifCompositionDist(multi, params) {
+    const { ct, motifs, datasetClass, maxDist = 20 } = params;
+    return multiMotifComposition(multi, ct, motifs, datasetClass, context => radiusNeighborhood(context, maxDist));
+}
+// Normalize motifs as differential_analysis_motif_* does (no filtering of unknown cell types).
+function toDifferentialMotifs(motifs) {
+    if (typeof motifs === 'string')
+        return [[motifs]];
+    if (motifs.length > 0 && typeof motifs[0] === 'string')
+        return [motifs];
+    return motifs;
+}
+// Test every motif for a difference in support between the datasets of two classes.
+// Returns all tested motifs, unlike differentialAnalysisKnn/Dist which return only the significant ones.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_differential_pattern.py
+function differentialTests(multi, datasetClasses, ct, motifsParam, 
+// Support of each motif among the given center cells of a dataset.
+supportsInFov) {
+    const motifs = [];
+    const motifKeys = new Set();
+    for (const motif of toDifferentialMotifs(motifsParam)) {
+        const sorted = motif.toSorted();
+        const key = JSON.stringify(sorted);
+        if (!motifKeys.has(key)) {
+            motifKeys.add(key);
+            motifs.push(sorted);
+        }
+    }
+    const supports = motifs.map(() => Object.fromEntries(datasetClasses.map(c => [c, []])));
+    for (const datasetClass of datasetClasses) {
+        for (const { context } of selectFovs(multi, datasetClass)) {
+            const cinds = findCellIndicesOfType(context, ct);
+            const fovSupports = cinds.length === 0 ? motifs.map(() => 0) : supportsInFov(context, cinds, motifs);
+            fovSupports.forEach((s, m) => supports[m][datasetClass].push(s));
+        }
+    }
+    const [c0, c1] = datasetClasses;
+    const results = motifs.map((itemsets, m) => {
+        const group1 = supports[m][c0];
+        const group2 = supports[m][c1];
+        let pValue = 1.0;
+        let datasetClassHigherFrequency = 'neither';
+        if (group1.length > 0 && group2.length > 0) {
+            pValue = mannWhitneyU(group1, group2).pValue;
+            // Determine which class has higher frequency using the median rank.
+            const ranks = rankAverage([...group1, ...group2]);
+            const medianRank1 = median(ranks.slice(0, group1.length));
+            const medianRank2 = median(ranks.slice(group1.length));
+            datasetClassHigherFrequency = medianRank1 > medianRank2 ? c0 : c1;
+        }
+        return {
+            itemsets,
+            supports: supports[m],
+            supportMean: { [c0]: mean(group1), [c1]: mean(group2) },
+            pValue,
+            datasetClassHigherFrequency,
+        };
+    });
+    if (results.length > 1) {
+        const { rejected, adjusted } = fdrCorrection(results.map(r => r.pValue), 0.05);
+        return results.map((r, i) => ({ ...r, adjPValue: adjusted[i], ifSignificant: rejected[i] }));
+    }
+    return results.map(r => ({ ...r, adjPValue: r.pValue, ifSignificant: r.pValue < 0.05 }));
+}
+// Split the significant results by the class with the higher frequency, sorted by adjusted p-value.
+function splitSignificant(results, datasetClasses) {
+    return Object.fromEntries(datasetClasses.map(c => [
+        c,
+        results
+            .filter(r => r.datasetClassHigherFrequency === c && r.ifSignificant)
+            .map(({ itemsets, supportMean, adjPValue }) => ({ itemsets, supportMean, adjPValue }))
+            .toSorted((a, b) => a.adjPValue - b.adjPValue),
+    ]));
+}
+// Union of the frequent patterns discovered in each dataset of the two classes.
+async function discoverMotifs(multi, datasetClasses, findFpFov) {
+    const motifs = new Map();
+    for (const datasetClass of datasetClasses) {
+        for (const { datasetId } of selectFovs(multi, datasetClass)) {
+            for (const { itemsets } of await findFpFov(datasetId)) {
+                motifs.set(JSON.stringify(itemsets.toSorted()), itemsets.toSorted());
+            }
+        }
+    }
+    return Array.from(motifs.values());
+}
+function validateDifferentialClasses(multi, datasetClasses) {
+    if (datasetClasses.length !== 2) {
+        throw new Error("Require 2 dataset classes for differential analysis.");
+    }
+    selectFovs(multi, datasetClasses);
+}
+// Fraction of the center cells whose neighborhood contains every motif cell type
+// (0 for motifs with a cell type missing from the dataset).
+function motifSupports(context, cinds, motifs, neighborsOf, isValidCenter = () => true) {
+    const labelsUnique = new Set(context.labels);
+    const neighborTypes = cinds.map((i) => {
+        const neighbors = neighborsOf(i);
+        return isValidCenter(neighbors) ? new Set(neighbors.map(j => context.labels[j])) : null;
+    });
+    return motifs.map((motif) => {
+        if (!motif.every(t => labelsUnique.has(t)))
+            return 0;
+        const count = neighborTypes.filter(types => types !== null && motif.every(t => types.has(t))).length;
+        return count / cinds.length;
+    });
+}
+// Test all motifs for differential support between two dataset classes using k-NN neighborhoods.
+// Returns every tested motif (including non-significant ones).
+export async function differentialTestsKnn(multi, params) {
+    const { ct, datasetClasses, k = 30, minSupport = 0.5, maxDist = 20 } = params;
+    validateDifferentialClasses(multi, datasetClasses);
+    const motifs = params.motifs ?? await discoverMotifs(multi, datasetClasses, datasetId => (findFpKnnFov(multi, { ct, datasetId, k, minSupport, maxDist })));
+    return differentialTests(multi, datasetClasses, ct, motifs, (context, cinds, ms) => (motifSupports(context, cinds, ms, knnNeighborhood(context, k, maxDist))));
+}
+// Perform differential analysis of motif patterns between two dataset classes using k-NN neighborhoods.
+// Returns, for each class, the motifs significantly more frequent in that class.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L1105
+export async function differentialAnalysisKnn(multi, params) {
+    return splitSignificant(await differentialTestsKnn(multi, params), params.datasetClasses);
+}
+// Test all motifs for differential support between two dataset classes using radius-based neighborhoods.
+// Returns every tested motif (including non-significant ones).
+export async function differentialTestsDist(multi, params) {
+    const { ct, datasetClasses, maxDist = 20, minSupport = 0.5, minSize = 0 } = params;
+    validateDifferentialClasses(multi, datasetClasses);
+    const motifs = params.motifs ?? await discoverMotifs(multi, datasetClasses, datasetId => (findFpDistFov(multi, { ct, datasetId, maxDist, minSize, minSupport })));
+    // Center cells with neighborhoods not larger than minSize never count as having the motif,
+    // but still count in the denominator of the support.
+    return differentialTests(multi, datasetClasses, ct, motifs, (context, cinds, ms) => (motifSupports(context, cinds, ms, radiusNeighborhood(context, maxDist), neighbors => neighbors.length > minSize)));
+}
+// Perform differential analysis of motif patterns between two dataset classes using radius-based neighborhoods.
+// Returns, for each class, the motifs significantly more frequent in that class.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query_multiple_fov.py#L1206
+export async function differentialAnalysisDist(multi, params) {
+    return splitSignificant(await differentialTestsDist(multi, params), params.datasetClasses);
+}
+//# sourceMappingURL=multi-fov.js.map

package/dist/multi-fov.js.map

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package/dist/nested.d.ts

@@ -0,0 +1,17 @@
+import { type FrequentPattern } from './fpgrowth.js';
+type TestedMotif = {
+    motifs: string[];
+    pValue: number;
+    adjPValue?: number;
+    ifSignificant?: boolean;
+};
+type NestedMotifDescentParams<T> = {
+    testMotifs: (motifs: string[][]) => Promise<T[]>;
+    frequentPatterns: FrequentPattern[];
+    supportTol?: number;
+    maxTestedPatterns?: number;
+    maxExpansionFactor?: number;
+};
+export declare function nestedMotifDescent<T extends TestedMotif>(params: NestedMotifDescentParams<T>): Promise<T[]>;
+export {};
+//# sourceMappingURL=nested.d.ts.map

package/dist/nested.d.ts.map

@@ -0,0 +1 @@
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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

@@ -0,0 +1 @@
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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