spatialquery.js 0.0.0-stage → 0.1.0

package/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Mark Keller
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

@@ -1,3 +1,139 @@
-# Temporary Holding Version
+# spatial-query.js
+JavaScript implementation of [Spatial-Query](https://github.com/ShaokunAn/Spatial-Query).
 
-This version is a temporary placeholder for this package. An operational version to replace this has been submitted for review and is awaiting a staged release.
+
+## Citation
+
+If you use SpatialQuery in your research, please cite the [preprint](https://doi.org/10.64898/2026.04.22.720136):
+
+
+> Shaokun An, Mark Keller, Nils Gehlenborg, Martin Hemberg. **SpatialQuery: scalable discovery and molecular characterization of multicellular motifs from spatial omics data.** bioRxiv. doi: 10.64898/2026.04.22.720136
+
+
+## Installation
+
+```sh
+npm install spatialquery.js
+```
+
+## Usage
+
+### Single field of view
+
+```js
+import {
+  buildContext,
+  findPatternsGrid,
+  motifEnrichmentDist,
+  motifCompositionDist,
+} from 'spatial-query';
+
+// Cell type label of each cell.
+const obsIdToLabel = new Map(obsIndex.map((obsId, i) => [obsId, labels[i]]));
+
+const context = buildContext({
+  obsIndex,          // string[] of cell IDs
+  xCoords,           // Float32Array | Float64Array
+  yCoords,           // Float32Array | Float64Array
+  obsIdToObsSetName: obsId => obsIdToLabel.get(obsId),
+  // By default, coordinates are normalized so the mean nearest-neighbor distance is 1.
+  normalizeSpatialCoord: true,
+});
+
+// Frequent cell type patterns around grid points.
+const patterns = await findPatternsGrid(context, { maxDist: 20, minSupport: 0.5 });
+// => [{ itemsets: ['B cell', 'T cell'], support: 0.62 }, ...]
+
+// Motifs enriched around a center cell type (k-NN version: motifEnrichmentKnn).
+const enrichment = await motifEnrichmentDist(context, {
+  ct: 'T cell',
+  maxDist: 20,
+  returnCellIds: true,  // adds centerIds / neighborIds (obs IDs) to each result
+});
+// => [{ center, motifs, nCenterMotif, nCenter, nMotif, expectation, pValue, adjPValue, ifSignificant, ... }]
+
+// Composition of a motif in the neighborhoods of the center cells.
+const composition = motifCompositionDist(context, {
+  ct: 'T cell',
+  motifs: enrichment[0].motifs,
+  maxDist: 20,
+});
+```
+
+Other functions: `findPatternsRand`, `findFpKnn`, `findFpDist`, `motifEnrichmentKnn`, `motifCompositionKnn`.
+The enrichment functions also accept `motifs` (to test specific motifs) and `mode: 'nested'` (to also test sub-patterns of non-significant motifs).
+
+### Multiple fields of view
+
+```js
+import {
+  buildMultiContext,
+  multiMotifEnrichmentKnn,
+  differentialAnalysisKnn,
+} from 'spatial-query';
+
+// One entry per FOV, with a unique dataset ID and a class (e.g., condition) shared by related FOVs.
+const multi = buildMultiContext([
+  { datasetId: 'sample-1', datasetClass: 'control', obsIndex: obsIndex1, xCoords: x1, yCoords: y1, obsIdToObsSetName: toLabel1 },
+  { datasetId: 'sample-2', datasetClass: 'control', obsIndex: obsIndex2, xCoords: x2, yCoords: y2, obsIdToObsSetName: toLabel2 },
+  { datasetId: 'sample-3', datasetClass: 'disease', obsIndex: obsIndex3, xCoords: x3, yCoords: y3, obsIdToObsSetName: toLabel3 },
+  // ...
+]);
+
+// Enrichment pooled across the FOVs of the selected classes (all FOVs by default).
+// With returnCellIds: true, cell IDs are keyed by dataset ID.
+const enrichment = await multiMotifEnrichmentKnn(multi, { ct: 'T cell', k: 30, maxDist: 20, datasetClass: 'disease' });
+
+// Motifs whose support differs significantly between the FOVs of two classes.
+const differential = await differentialAnalysisKnn(multi, {
+  ct: 'T cell',
+  datasetClasses: ['control', 'disease'],
+});
+// => { control: [{ itemsets, supportMean, adjPValue }, ...], disease: [...] }
+```
+
+Other functions: `multiFindFpKnn`, `multiFindFpDist`, `findFpKnnFov` / `findFpDistFov` (one FOV, by `datasetId`), `multiMotifEnrichmentDist`, `multiMotifCompositionKnn`, `multiMotifCompositionDist`, `differentialAnalysisDist`, and `differentialTestsKnn` / `differentialTestsDist` (all tested motifs, not only the significant ones).
+
+
+## Development
+
+### Setup
+
+```sh
+pnpm install
+```
+
+Download the test fixture files and run the Python fixture conversion/generation scripts:
+
+```sh
+cd fixtures
+# The HuBMAP assets server rejects curl's default User-Agent.
+curl -fL -A "Mozilla/5.0" -o secondary_analysis.h5ad https://assets.hubmapconsortium.org/0a21f3fa27109790483f2a0729be53de/secondary_analysis.h5ad
+CC=/usr/bin/clang CXX=/usr/bin/clang++ uv run test_find_patterns_grid.py
+CC=/usr/bin/clang CXX=/usr/bin/clang++ uv run generate_motif_fixtures.py
+CC=/usr/bin/clang CXX=/usr/bin/clang++ uv run generate_multi_fov_fixtures.py
+cd ..
+```
+
+### Testing
+
+The tests compare the JS outputs to Python reference outputs. See [fixtures/README.md](fixtures/README.md) to download the test data and generate the reference outputs, then:
+
+```sh
+pnpm test
+```
+
+### Publish to NPM
+
+```sh
+pnpm run build
+
+npm login
+pnpm publish --no-git-checks --provenance --access public
+```
+
+## Related work
+
+Related to:
+- Initial implementation work in [vitessce#2116](https://github.com/vitessce/vitessce/pull/2116/).
+- Widget plugin in [vitessce-python](https://github.com/vitessce/vitessce-python/blob/main/src/vitessce/widget_plugins/spatial_query.py) ([example notebook](https://github.com/vitessce/vitessce-python/blob/main/docs/notebooks/widget_plugin_spatial-query.ipynb))

package/dist/assert.d.ts

@@ -0,0 +1,15 @@
+/**
+ * Error thrown when an assertion fails.
+ */
+export declare class AssertionError extends Error {
+    /** @param message The error message. */
+    constructor(message: string);
+}
+/**
+ * Make an assertion. An error is thrown if `expr` does not have truthy value.
+ *
+ * @param expr The expression to test.
+ * @param msg The message to display if the assertion fails.
+ */
+export declare function assert(expr: unknown, msg?: string): asserts expr;
+//# sourceMappingURL=assert.d.ts.map

package/dist/assert.d.ts.map

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package/dist/assert.js

@@ -0,0 +1,23 @@
+// Reference: https://github.com/hms-dbmi/vizarr/blob/82756a8604b1612aa35bb8a292c1451ee9647b70/src/utils.ts#L434
+/**
+ * Error thrown when an assertion fails.
+ */
+export class AssertionError extends Error {
+    /** @param message The error message. */
+    constructor(message) {
+        super(message);
+        this.name = "AssertionError";
+    }
+}
+/**
+ * Make an assertion. An error is thrown if `expr` does not have truthy value.
+ *
+ * @param expr The expression to test.
+ * @param msg The message to display if the assertion fails.
+ */
+export function assert(expr, msg = "") {
+    if (!expr) {
+        throw new AssertionError(msg);
+    }
+}
+//# sourceMappingURL=assert.js.map

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package/dist/fpgrowth.d.ts

@@ -0,0 +1,10 @@
+export type FrequentPattern = {
+    itemsets: string[];
+    support: number;
+    neighborIds?: string[];
+};
+export declare function findMaximalPatterns<T extends {
+    itemsets: string[];
+}>(patterns: T[]): T[];
+export declare function mineFrequentPatterns(transactions: string[][], minSupport: number, ifMax: boolean): Promise<FrequentPattern[]>;
+//# sourceMappingURL=fpgrowth.d.ts.map

package/dist/fpgrowth.d.ts.map

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package/dist/fpgrowth.js

@@ -0,0 +1,35 @@
+import { FPGrowth } from 'node-fpgrowth';
+// Keep only the maximal patterns: those that are not a proper subset of another pattern.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_utils.py#L68
+export function findMaximalPatterns(patterns) {
+    const sets = patterns.map(p => new Set(p.itemsets));
+    return patterns.filter((p, i) => !sets.some((other, j) => (j !== i
+        && other.size > sets[i].size
+        && p.itemsets.every(item => other.has(item)))));
+}
+// Mine frequent patterns from transactions of cell type labels.
+// Equivalent to the MultiLabelBinarizer + mlxtend fpgrowth + find_maximal_patterns
+// steps of build_fptree_dist / build_fptree_knn.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_utils.py#L454
+export async function mineFrequentPatterns(transactions, minSupport, ifMax) {
+    if (transactions.length === 0) {
+        return [];
+    }
+    // Transactions are binarized in Python, so duplicate cell types are collapsed.
+    const uniqueTransactions = transactions.map(t => Array.from(new Set(t)));
+    const fpgrowth = new FPGrowth(minSupport);
+    const itemsets = await fpgrowth.exec(uniqueTransactions);
+    // node-fpgrowth reports support as a count; mlxtend reports a fraction.
+    const byKey = new Map();
+    for (const { items, support } of itemsets) {
+        const sorted = items.toSorted();
+        byKey.set(JSON.stringify(sorted), { itemsets: sorted, support: support / transactions.length });
+    }
+    let patterns = Array.from(byKey.values());
+    if (ifMax) {
+        patterns = findMaximalPatterns(patterns);
+    }
+    // Sort by descending support, breaking ties by itemsets for a deterministic order.
+    return patterns.toSorted((a, b) => (b.support - a.support || JSON.stringify(a.itemsets).localeCompare(JSON.stringify(b.itemsets))));
+}
+//# sourceMappingURL=fpgrowth.js.map

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package/dist/index.d.ts

@@ -0,0 +1,6 @@
+export { generateObsIdToObsSetName, normalizeSpatialCoords, buildContext, buildGridPoints, findPatternsGrid, findPatternsRand, findFpKnn, findFpDist, computeMotifEnrichment, motifEnrichmentKnn, motifEnrichmentDist, motifCompositionKnn, motifCompositionDist, type InitParams, type SqContext, type MotifsParam, type EnrichmentMode, type MotifEnrichmentResult, type MotifCompositionRow, } from './single-fov.js';
+export { buildMultiContext, multiFindFpKnn, multiFindFpDist, findFpKnnFov, findFpDistFov, multiMotifEnrichmentKnn, multiMotifEnrichmentDist, multiMotifCompositionKnn, multiMotifCompositionDist, differentialAnalysisKnn, differentialAnalysisDist, differentialTestsKnn, differentialTestsDist, type FovInitParams, type SqMultiContext, type MultiFovMotifEnrichmentResult, type MultiFovMotifCompositionRow, type DifferentialResult, type DifferentialTestResult, } from './multi-fov.js';
+export { findMaximalPatterns, type FrequentPattern } from './fpgrowth.js';
+export { nestedMotifDescent } from './nested.js';
+export { applyFdrCorrection } from './stats.js';
+//# sourceMappingURL=index.d.ts.map

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package/dist/index.js

@@ -0,0 +1,6 @@
+export { generateObsIdToObsSetName, normalizeSpatialCoords, buildContext, buildGridPoints, findPatternsGrid, findPatternsRand, findFpKnn, findFpDist, computeMotifEnrichment, motifEnrichmentKnn, motifEnrichmentDist, motifCompositionKnn, motifCompositionDist, } from './single-fov.js';
+export { buildMultiContext, multiFindFpKnn, multiFindFpDist, findFpKnnFov, findFpDistFov, multiMotifEnrichmentKnn, multiMotifEnrichmentDist, multiMotifCompositionKnn, multiMotifCompositionDist, differentialAnalysisKnn, differentialAnalysisDist, differentialTestsKnn, differentialTestsDist, } from './multi-fov.js';
+export { findMaximalPatterns } from './fpgrowth.js';
+export { nestedMotifDescent } from './nested.js';
+export { applyFdrCorrection } from './stats.js';
+//# sourceMappingURL=index.js.map

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package/dist/multi-fov.d.ts

@@ -0,0 +1,115 @@
+import { type InitParams, type SqContext, type MotifsParam, type MotifEnrichmentResult, type MotifCompositionRow, type EnrichmentMode } from './single-fov.js';
+import { type FrequentPattern } from './fpgrowth.js';
+export type FovInitParams = InitParams & {
+    datasetId: string;
+    datasetClass: string;
+};
+export type SqMultiContext = {
+    datasetIds: string[];
+    datasetClasses: string[];
+    contexts: SqContext[];
+};
+export declare function buildMultiContext(fovs: FovInitParams[]): SqMultiContext;
+type DatasetClassParam = {
+    datasetClass?: string | string[];
+};
+type MultiFindFpKnnParams = DatasetClassParam & {
+    ct: string;
+    k?: number;
+    minSupport?: number;
+    maxDist?: number;
+    ifMax?: boolean;
+};
+export declare function multiFindFpKnn(multi: SqMultiContext, params: MultiFindFpKnnParams): Promise<FrequentPattern[]>;
+type MultiFindFpDistParams = DatasetClassParam & {
+    ct: string;
+    maxDist?: number;
+    minSize?: number;
+    minSupport?: number;
+    ifMax?: boolean;
+};
+export declare function multiFindFpDist(multi: SqMultiContext, params: MultiFindFpDistParams): Promise<FrequentPattern[]>;
+type FindFpFovParams = {
+    ct: string;
+    datasetId: string;
+};
+export declare function findFpKnnFov(multi: SqMultiContext, params: FindFpFovParams & {
+    k?: number;
+    minSupport?: number;
+    maxDist?: number;
+}): Promise<FrequentPattern[]>;
+export declare function findFpDistFov(multi: SqMultiContext, params: FindFpFovParams & {
+    maxDist?: number;
+    minSize?: number;
+    minSupport?: number;
+}): Promise<FrequentPattern[]>;
+export type MultiFovMotifEnrichmentResult = Omit<MotifEnrichmentResult, 'neighborIds' | 'centerIds'> & {
+    neighborIds?: Record<string, string[]>;
+    centerIds?: Record<string, string[]>;
+};
+type MultiMotifEnrichmentKnnParams = DatasetClassParam & {
+    ct: string;
+    motifs?: MotifsParam;
+    k?: number;
+    minSupport?: number;
+    maxDist?: number;
+    returnCellIds?: boolean;
+    mode?: EnrichmentMode;
+};
+export declare function multiMotifEnrichmentKnn(multi: SqMultiContext, params: MultiMotifEnrichmentKnnParams): Promise<MultiFovMotifEnrichmentResult[]>;
+type MultiMotifEnrichmentDistParams = DatasetClassParam & {
+    ct: string;
+    motifs?: MotifsParam;
+    maxDist?: number;
+    minSize?: number;
+    minSupport?: number;
+    returnCellIds?: boolean;
+    mode?: EnrichmentMode;
+};
+export declare function multiMotifEnrichmentDist(multi: SqMultiContext, params: MultiMotifEnrichmentDistParams): Promise<MultiFovMotifEnrichmentResult[]>;
+export type MultiFovMotifCompositionRow = MotifCompositionRow & {
+    datasetId: string;
+};
+export declare function multiMotifCompositionKnn(multi: SqMultiContext, params: DatasetClassParam & {
+    ct: string;
+    motifs: MotifsParam;
+    k?: number;
+    maxDist?: number;
+}): MultiFovMotifCompositionRow[];
+export declare function multiMotifCompositionDist(multi: SqMultiContext, params: DatasetClassParam & {
+    ct: string;
+    motifs: MotifsParam;
+    maxDist?: number;
+}): MultiFovMotifCompositionRow[];
+export type DifferentialTestResult = {
+    itemsets: string[];
+    supports: Record<string, number[]>;
+    supportMean: Record<string, number>;
+    pValue: number;
+    adjPValue: number;
+    ifSignificant: boolean;
+    datasetClassHigherFrequency: string;
+};
+export type DifferentialResult = Pick<DifferentialTestResult, 'itemsets' | 'supportMean' | 'adjPValue'>;
+type DifferentialAnalysisKnnParams = {
+    ct: string;
+    datasetClasses: string[];
+    motifs?: MotifsParam;
+    k?: number;
+    minSupport?: number;
+    maxDist?: number;
+};
+export declare function differentialTestsKnn(multi: SqMultiContext, params: DifferentialAnalysisKnnParams): Promise<DifferentialTestResult[]>;
+export declare function differentialAnalysisKnn(multi: SqMultiContext, params: DifferentialAnalysisKnnParams): Promise<Record<string, DifferentialResult[]>>;
+type DifferentialAnalysisDistParams = {
+    ct: string;
+    datasetClasses: string[];
+    motifs?: MotifsParam;
+    maxDist?: number;
+    minSupport?: number;
+    minSize?: number;
+};
+export declare function differentialTestsDist(multi: SqMultiContext, params: DifferentialAnalysisDistParams): Promise<DifferentialTestResult[]>;
+export declare function differentialAnalysisDist(multi: SqMultiContext, params: DifferentialAnalysisDistParams): Promise<Record<string, DifferentialResult[]>>;
+export {};
+//# sourceMappingURL=multi-fov.d.ts.map

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

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