spatialquery.js 0.0.0-stage → 0.1.0

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

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package/dist/single-fov.js

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+import Flatbush from 'flatbush';
+import { extent } from 'd3-array';
+import { assert } from './assert.js';
+import { hypergeom, roundHalfEven, applyFdrCorrection } from './stats.js';
+import { mineFrequentPatterns } from './fpgrowth.js';
+import { nestedMotifDescent } from './nested.js';
+export function generateObsIdToObsSetName(obsSetsMembership, currSelectedSetGroup) {
+    // Function that accepts an obsId and returns a single string representing the cell type name.
+    return (obsId) => {
+        const obsIdCellType = obsSetsMembership.get(obsId)
+            ?.find(setPath => setPath[0] === currSelectedSetGroup)?.[1]; // Again, we take the second element of the setPath as the cell type name
+        assert(typeof obsIdCellType === 'string', "Result of obsIdToObsSetName was falsey");
+        return obsIdCellType;
+    };
+}
+// Scale spatial coordinates so that the mean nearest neighbor distance equals 1.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/0570c54bd6e046466e05c6b800d6701a7ab15c4a/SpatialQuery/spatial_utils.py#L804
+export function normalizeSpatialCoords(xCoords, yCoords) {
+    const numCells = xCoords.length;
+    assert(numCells >= 2, "At least two cells are required to normalize spatial coordinates.");
+    // Temporary spatial index over the original coordinates, used to find each cell's nearest neighbor.
+    const index = new Flatbush(numCells);
+    for (let i = 0; i < numCells; i++) {
+        index.add(xCoords[i], yCoords[i]);
+    }
+    index.finish();
+    let nnDistSum = 0;
+    for (let i = 0; i < numCells; i++) {
+        // Exclude the cell itself (equivalent to taking the second result of a k=2 KDTree query).
+        const [j] = index.neighbors(xCoords[i], yCoords[i], 1, Infinity, (j) => j !== i);
+        nnDistSum += Math.hypot(xCoords[i] - xCoords[j], yCoords[i] - yCoords[j]);
+    }
+    const nnDist = nnDistSum / numCells;
+    assert(nnDist > 0, "Mean nearest neighbor distance was zero; cannot normalize spatial coordinates.");
+    const scaleFactor = 1.0 / nnDist;
+    return {
+        xCoords: Float64Array.from(xCoords, x => x * scaleFactor),
+        yCoords: Float64Array.from(yCoords, y => y * scaleFactor),
+        scaleFactor,
+    };
+}
+// Build the context object.
+export function buildContext(params) {
+    const { obsIndex, // Array of each obs ID, as a string.
+    xCoords: rawXCoords, // TypedArray containing X coordinate of each cell (centroid)
+    yCoords: rawYCoords, // TypedArray containing Y coordinate of each cell (centroid)
+    obsIdToObsSetName, // Function mapping an obs ID to its cell type label.
+    leafSize = 10, // Leaf size parameter for KDTree construction. Larger values reduce tree depth but increase computation per query.
+    normalizeSpatialCoord = true, // If True, normalizes spatial coordinates so mean nearest neighbor distance equals 1. This makes max_dist parameter interpretable as “number of cell diameters.” Set to False if original spatial units (e.g., micrometers) are required and should be preserved for downstream analysis.
+     } = params;
+    const { xCoords, yCoords } = normalizeSpatialCoord
+        ? normalizeSpatialCoords(rawXCoords, rawYCoords)
+        : { xCoords: rawXCoords, yCoords: rawYCoords };
+    const xExtent = extent(xCoords);
+    const yExtent = extent(yCoords);
+    assert(typeof xExtent[0] === 'number' && typeof xExtent[1] === 'number', "X extent min or max was undefined.");
+    assert(typeof yExtent[0] === 'number' && typeof yExtent[1] === 'number', "Y extent min or max was undefined.");
+    // Initialize Flatbush for N items
+    const flatbushIndex = new Flatbush(obsIndex.length, leafSize);
+    for (let i = 0; i < obsIndex.length; i++) {
+        flatbushIndex.add(xCoords[i], yCoords[i]);
+    }
+    // perform the indexing
+    flatbushIndex.finish();
+    return {
+        obsIndex,
+        labels: obsIndex.map(obsId => obsIdToObsSetName(obsId)),
+        xCoords,
+        yCoords,
+        xExtent,
+        yExtent,
+        flatbushIndex,
+    };
+}
+// ---------------------------------------------------------------------------
+// Neighborhood queries
+// ---------------------------------------------------------------------------
+// Indices of cells within maxDist (inclusive) of a point, like KDTree.query_ball_point.
+function radiusNeighbors(context, x, y, maxDist) {
+    return context.flatbushIndex.neighbors(x, y, Infinity, maxDist);
+}
+// The k nearest neighbors of cell i (excluding itself) and their distances,
+// like KDTree.query(k=k+1) with the first result (the cell itself) dropped.
+function knnNeighbors(context, i, k) {
+    const { xCoords, yCoords, flatbushIndex } = context;
+    const x = xCoords[i];
+    const y = yCoords[i];
+    const indices = flatbushIndex.neighbors(x, y, k, Infinity, j => j !== i);
+    const dists = indices.map(j => Math.hypot(xCoords[j] - x, yCoords[j] - y));
+    return { indices, dists };
+}
+// Indices of the cells annotated with the cell type ct (possibly none).
+export function findCellIndicesOfType(context, ct) {
+    const cinds = [];
+    context.labels.forEach((label, i) => {
+        if (label === ct)
+            cinds.push(i);
+    });
+    return cinds;
+}
+// Indices of the cells annotated with the cell type ct, throwing if there are none.
+function getCellIndicesOfType(context, ct) {
+    const cinds = findCellIndicesOfType(context, ct);
+    if (cinds.length === 0) {
+        throw new Error(`Found no ${ct} in the cell type labels!`);
+    }
+    return cinds;
+}
+// Neighborhood of each cell (excluding the cell itself) used by the k-NN motif enrichment and composition:
+// the k nearest neighbors within maxDist (inclusive).
+export function knnNeighborhood(context, k, maxDist) {
+    return (i) => {
+        const { indices, dists } = knnNeighbors(context, i, k);
+        return indices.filter((_, n) => dists[n] <= maxDist);
+    };
+}
+// Neighborhood of each cell (excluding the cell itself) used by the radius-based motif enrichment and composition.
+export function radiusNeighborhood(context, maxDist) {
+    const { xCoords, yCoords } = context;
+    return (i) => radiusNeighbors(context, xCoords[i], yCoords[i], maxDist).filter(j => j !== i);
+}
+// Cell type transactions for the radius-based neighborhood of each query point.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_utils.py#L393
+export function radiusTransactions(context, points, maxDist, minSize) {
+    const transactions = [];
+    const neighborLists = [];
+    for (const { x, y, exclude } of points) {
+        const idx = radiusNeighbors(context, x, y, maxDist);
+        if (idx.length === 0)
+            continue;
+        const validIndices = idx.filter(j => j !== exclude);
+        // Python compares the number of neighbor cells (not unique cell types) against min_size.
+        if (validIndices.length > minSize) {
+            transactions.push(validIndices.map(j => context.labels[j]));
+            neighborLists.push(validIndices);
+        }
+    }
+    return { transactions, neighborLists };
+}
+// Cell type transactions for the k-NN neighborhood of each center cell.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_utils.py#L475
+export function knnTransactions(context, cinds, k, maxDist) {
+    const transactions = [];
+    // In Python, the center cell itself (at distance 0) must pass the dist < max_dist filter,
+    // otherwise the neighborhood is skipped entirely. Neighborhoods may otherwise be empty.
+    if (!(maxDist > 0)) {
+        return transactions;
+    }
+    for (const i of cinds) {
+        const { indices, dists } = knnNeighbors(context, i, k);
+        // Note: strict inequality here, unlike in motif_enrichment_knn.
+        transactions.push(indices.filter((_, n) => dists[n] < maxDist).map(j => context.labels[j]));
+    }
+    return transactions;
+}
+// For each pattern, collect the cells (with cell types in the pattern) from the
+// neighborhoods that contain the full pattern.
+function attachNeighborIds(context, patterns, transactions, neighborLists) {
+    const transactionSets = transactions.map(t => new Set(t));
+    return patterns.map((pattern) => {
+        const motif = new Set(pattern.itemsets);
+        const ids = new Set();
+        transactionSets.forEach((transaction, t) => {
+            if (pattern.itemsets.every(ct => transaction.has(ct))) {
+                for (const j of neighborLists[t]) {
+                    if (motif.has(context.labels[j]))
+                        ids.add(j);
+                }
+            }
+        });
+        const neighborIds = Array.from(ids).sort((a, b) => a - b).map(j => context.obsIndex[j]);
+        return { ...pattern, neighborIds };
+    });
+}
+async function findPatternsAtPoints(context, points, params) {
+    const { maxDist = 20, minSize = 0, minSupport = 0.5, returnCellIds = false, } = params;
+    // Note: Python (build_fptree_dist with cinds=None) also excludes the cell whose index
+    // equals the index of the query point. We do not reproduce that quirk.
+    const queryPoints = points.map(([x, y]) => ({ x, y }));
+    const { transactions, neighborLists } = radiusTransactions(context, queryPoints, maxDist, minSize);
+    const patterns = await mineFrequentPatterns(transactions, minSupport, true);
+    if (returnCellIds) {
+        return attachNeighborIds(context, patterns, transactions, neighborLists);
+    }
+    return patterns;
+}
+// Equivalent to np.arange(start, stop, step).
+function arange(start, stop, step) {
+    const n = Math.max(0, Math.ceil((stop - start) / step));
+    return Array.from({ length: n }, (_, i) => start + i * step);
+}
+// Grid points used by findPatternsGrid, with spacing maxDist.
+// Equivalent to the grid returned by find_patterns_grid(return_grid=True).
+export function buildGridPoints(context, maxDist = 20) {
+    const { xExtent, yExtent } = context;
+    const xGrid = arange(xExtent[0] - maxDist, xExtent[1] + maxDist, maxDist);
+    const yGrid = arange(yExtent[0] - maxDist, yExtent[1] + maxDist, maxDist);
+    const gridPoints = [];
+    for (const x of xGrid) {
+        for (const y of yGrid) {
+            gridPoints.push([x, y]);
+        }
+    }
+    return gridPoints;
+}
+// Create a grid and use it to find surrounding patterns in spatial data.
+// Reference: https://spatialquery.readthedocs.io/en/latest/generated/SpatialQuery.spatial_query.find_patterns_grid.html
+export async function findPatternsGrid(context, params = {}) {
+    const { maxDist = 20 } = params;
+    return findPatternsAtPoints(context, buildGridPoints(context, maxDist), params);
+}
+// Randomly generate points and use them to find surrounding patterns in spatial data.
+// Uses Math.random, so results will not exactly match Python (which uses a seeded numpy RNG).
+// Reference: https://spatialquery.readthedocs.io/en/latest/generated/SpatialQuery.spatial_query.find_patterns_rand.html
+export async function findPatternsRand(context, params = {}) {
+    const { nPoints = 1000 } = params;
+    const { xExtent: [xMin, xMax], yExtent: [yMin, yMax] } = context;
+    // As in Python, all x coordinates are drawn before all y coordinates.
+    const xs = Array.from({ length: nPoints }, () => Math.random() * (xMax - xMin) + xMin);
+    const ys = Array.from({ length: nPoints }, () => Math.random() * (yMax - yMin) + yMin);
+    const points = xs.map((x, i) => [x, ys[i]]);
+    return findPatternsAtPoints(context, points, params);
+}
+// Find frequent patterns within the k-NN neighborhoods of a cell type.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query.py#L155
+export async function findFpKnn(context, params) {
+    const { ct, k = 30, minSupport = 0.5, maxDist = 20, ifMax = true } = params;
+    const cinds = getCellIndicesOfType(context, ct);
+    const transactions = knnTransactions(context, cinds, k, maxDist);
+    return mineFrequentPatterns(transactions, minSupport, ifMax);
+}
+// Find frequent patterns within the radius-based neighborhoods of a cell type.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query.py#L202
+export async function findFpDist(context, params) {
+    const { ct, maxDist = 20, minSize = 0, minSupport = 0.5, ifMax = true } = params;
+    const cinds = getCellIndicesOfType(context, ct);
+    const { transactions } = radiusTransactions(context, centerQueryPoints(context, cinds), maxDist, minSize);
+    return mineFrequentPatterns(transactions, minSupport, ifMax);
+}
+// Query points at the given cells, excluding each cell from its own neighborhood.
+export function centerQueryPoints(context, cinds) {
+    return cinds.map(i => ({ x: context.xCoords[i], y: context.yCoords[i], exclude: i }));
+}
+// Compute the hypergeometric enrichment test for a single motif,
+// given the neighborhood counts from a k-NN or radius-based query.
+// Currently, SpatialQuery only provides p-values for cellTypeOfInterest queries.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/0570c54bd6e046466e05c6b800d6701a7ab15c4a/SpatialQuery/spatial_query.py#L490C13-L492C131
+export function computeMotifEnrichment(params) {
+    const { center, motif, numCells, numCenter, numMotif, numCenterMotif, } = params;
+    // If the center cell type appears in the motif, divide by the number of times it appears.
+    // Python's round() rounds half to even, so we match that here.
+    let nCenter = numCenter;
+    const centerCount = motif.filter(ct => ct === center).length;
+    if (centerCount > 0) {
+        nCenter = roundHalfEven(nCenter / centerCount);
+    }
+    // M = total number of cells, n = number of "successes" (center cells),
+    // N = number drawn without replacement (cells with the motif in their neighborhood).
+    const hyge = hypergeom(numCells, nCenter, numMotif);
+    return {
+        center,
+        motifs: motif.toSorted(),
+        nCenterMotif: numCenterMotif,
+        nCenter,
+        nMotif: numMotif,
+        expectation: hyge.mean(),
+        pValue: hyge.sf(numCenterMotif),
+    };
+}
+// Turn a str / List[str] / List[List[str]] motifs argument into a list of motifs.
+function toMotifList(motifs) {
+    if (typeof motifs === 'string') {
+        return [[motifs]];
+    }
+    if (motifs.every(m => typeof m === 'string')) {
+        return [motifs];
+    }
+    return motifs;
+}
+// Normalize a motifs argument into a list of motifs, dropping cell types that are not
+// present in the data. Used by the motif enrichment functions (which keep the motif order and duplicates).
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query.py#L343
+export function normalizeMotifs(motifs, labelsUnique) {
+    const filteredMotifs = [];
+    for (const motif of toMotifList(motifs)) {
+        const motifExc = motif.filter(m => !labelsUnique.has(m));
+        if (motifExc.length > 0) {
+            console.warn(`Found no ${JSON.stringify(motifExc)} in the cell type labels. Ignoring them.`);
+        }
+        const validMotif = motif.filter(m => labelsUnique.has(m));
+        if (validMotif.length > 0) {
+            filteredMotifs.push(validMotif);
+        }
+    }
+    return filteredMotifs;
+}
+// Normalize a motifs argument into sorted, de-duplicated motifs, dropping cell types that are
+// not present in the data. Used by the motif composition functions.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_utils.py#L300
+export function normalizeMotifList(motifs, labelsUnique) {
+    return normalizeMotifs(motifs, labelsUnique).map(motif => Array.from(new Set(motif)).sort());
+}
+// Count, for each motif, the cells (and center cells) whose neighborhood contains every
+// cell type of the motif, given a function returning the neighborhood of each cell.
+// The center cell type may be absent (relevant for multi-FOV).
+export function countMotifs(context, ct, motifs, neighborsOf, returnCellIds) {
+    const { labels } = context;
+    const numCells = labels.length;
+    const cinds = findCellIndicesOfType(context, ct);
+    // Encode cell type labels as integers.
+    const labelsUnique = Array.from(new Set(labels)).sort();
+    const labelToCode = new Map(labelsUnique.map((label, code) => [label, code]));
+    const numTypes = labelsUnique.length;
+    // A motif with a cell type missing from this FOV cannot be present in any neighborhood.
+    const isActive = motifs.map(motif => motif.every(m => labelToCode.has(m)));
+    const emptyCounts = () => ({
+        numCells,
+        numCenter: cinds.length,
+        numMotif: 0,
+        numCenterMotif: 0,
+        ...(returnCellIds ? { centerIndices: [], neighborIndices: [] } : {}),
+    });
+    if (!isActive.some(Boolean)) {
+        return motifs.map(emptyCounts);
+    }
+    // Presence of each cell type in the neighborhood of each cell.
+    const codes = Int32Array.from(labels, label => labelToCode.get(label));
+    const presence = new Uint8Array(numCells * numTypes);
+    const centerNeighbors = new Map();
+    const isCenter = new Uint8Array(numCells);
+    for (const i of cinds)
+        isCenter[i] = 1;
+    for (let i = 0; i < numCells; i++) {
+        const neighbors = neighborsOf(i);
+        for (const j of neighbors) {
+            presence[i * numTypes + codes[j]] = 1;
+        }
+        if (returnCellIds && isCenter[i]) {
+            centerNeighbors.set(i, neighbors);
+        }
+    }
+    const hasMotif = (i, motifCodes) => motifCodes.every(c => presence[i * numTypes + c] === 1);
+    return motifs.map((motif, m) => {
+        if (!isActive[m]) {
+            return emptyCounts();
+        }
+        const motifCodes = Array.from(new Set(motif), t => labelToCode.get(t));
+        let numMotif = 0;
+        for (let i = 0; i < numCells; i++) {
+            if (hasMotif(i, motifCodes))
+                numMotif++;
+        }
+        const centersWithMotif = cinds.filter(i => hasMotif(i, motifCodes));
+        const counts = {
+            numCells,
+            numCenter: cinds.length,
+            numMotif,
+            numCenterMotif: centersWithMotif.length,
+        };
+        if (returnCellIds) {
+            const motifSet = new Set(motif);
+            const neighborIndices = new Set();
+            for (const i of centersWithMotif) {
+                for (const j of centerNeighbors.get(i)) {
+                    if (motifSet.has(labels[j]))
+                        neighborIndices.add(j);
+                }
+            }
+            counts.centerIndices = centersWithMotif;
+            counts.neighborIndices = Array.from(neighborIndices).sort((a, b) => a - b);
+        }
+        return counts;
+    });
+}
+// Run the enrichment test for each motif, given a function returning the
+// neighborhood (excluding the cell itself) of each cell.
+function motifEnrichment(context, ct, motifs, neighborsOf, returnCellIds) {
+    const { obsIndex } = context;
+    const counts = countMotifs(context, ct, motifs, neighborsOf, returnCellIds);
+    const out = motifs.map((motif, m) => {
+        const { numCells, numCenter, numMotif, numCenterMotif, centerIndices, neighborIndices } = counts[m];
+        const result = computeMotifEnrichment({ center: ct, motif, numCells, numCenter, numMotif, numCenterMotif });
+        if (returnCellIds) {
+            // Note: when no center cell has the motif, Python skips the motif entirely
+            // (it is dropped from the results). Here we keep it, with empty cell IDs.
+            result.neighborIds = neighborIndices.map(j => obsIndex[j]);
+            result.centerIds = centerIndices.map(i => obsIndex[i]);
+        }
+        return result;
+    });
+    return applyFdrCorrection(out);
+}
+export function assertEnrichmentMode(mode) {
+    if (mode !== 'maximal' && mode !== 'nested') {
+        throw new Error(`mode must be 'nested' or 'maximal', got '${mode}'`);
+    }
+}
+// Perform motif enrichment analysis using k-nearest neighbors.
+// Reference: https://spatialquery.readthedocs.io/en/latest/generated/SpatialQuery.spatial_query.motif_enrichment_knn.html
+export async function motifEnrichmentKnn(context, params) {
+    const { ct, k = 30, minSupport = 0.5, maxDist = 20, returnCellIds = false, mode = 'maximal' } = params;
+    getCellIndicesOfType(context, ct);
+    assertEnrichmentMode(mode);
+    if (mode === 'nested' && params.motifs === undefined) {
+        return nestedMotifDescent({
+            testMotifs: motifs => motifEnrichmentKnn(context, { ...params, motifs, mode: 'maximal' }),
+            frequentPatterns: await findFpKnn(context, { ct, k, minSupport, maxDist, ifMax: false }),
+        });
+    }
+    const motifs = params.motifs === undefined
+        ? (await findFpKnn(context, { ct, k, minSupport, maxDist })).map(p => p.itemsets)
+        : normalizeMotifs(params.motifs, new Set(context.labels));
+    if (motifs.length === 0) {
+        return [];
+    }
+    return motifEnrichment(context, ct, motifs, knnNeighborhood(context, k, maxDist), returnCellIds);
+}
+// Perform motif enrichment analysis within a radius-based neighborhood.
+// Reference: https://spatialquery.readthedocs.io/en/latest/generated/SpatialQuery.spatial_query.motif_enrichment_dist.html
+export async function motifEnrichmentDist(context, params) {
+    const { ct, maxDist = 20, minSize = 0, minSupport = 0.5, returnCellIds = false, mode = 'maximal' } = params;
+    getCellIndicesOfType(context, ct);
+    assertEnrichmentMode(mode);
+    if (mode === 'nested' && params.motifs === undefined) {
+        return nestedMotifDescent({
+            testMotifs: motifs => motifEnrichmentDist(context, { ...params, motifs, mode: 'maximal' }),
+            frequentPatterns: await findFpDist(context, { ct, maxDist, minSize, minSupport, ifMax: false }),
+        });
+    }
+    const motifs = params.motifs === undefined
+        ? (await findFpDist(context, { ct, maxDist, minSize, minSupport })).map(p => p.itemsets)
+        : normalizeMotifs(params.motifs, new Set(context.labels));
+    if (motifs.length === 0) {
+        return [];
+    }
+    return motifEnrichment(context, ct, motifs, radiusNeighborhood(context, maxDist), returnCellIds);
+}
+// Long-format composition of the motif-type cells in the neighborhoods of the center cells
+// (cinds) whose neighborhood contains every motif cell type: one row per (center cell, motif cell type).
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_utils.py#L362
+export function motifCompositionRows(context, ct, motifs, cinds, neighborsOf) {
+    const { labels } = context;
+    // Per-cell-type neighbor counts of each center cell.
+    const centerCounts = cinds.map((i) => {
+        const counts = new Map();
+        for (const j of neighborsOf(i)) {
+            counts.set(labels[j], (counts.get(labels[j]) ?? 0) + 1);
+        }
+        return counts;
+    });
+    const rows = [];
+    for (const motif of motifs) {
+        for (const counts of centerCounts) {
+            const motifCounts = motif.map(t => counts.get(t) ?? 0);
+            if (!motifCounts.every(c => c > 0))
+                continue;
+            const total = motifCounts.reduce((a, b) => a + b, 0);
+            motif.forEach((cellType, n) => {
+                rows.push({
+                    center: ct,
+                    motifs: motif,
+                    cellType,
+                    nCells: motifCounts[n],
+                    nMotifCells: total,
+                    proportion: motifCounts[n] / total,
+                });
+            });
+        }
+    }
+    return rows;
+}
+// Compute the composition of motif cell types in the k-NN neighborhoods of center cells.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query.py#L681
+export function motifCompositionKnn(context, params) {
+    const { ct, k = 30, maxDist = 20 } = params;
+    const cinds = getCellIndicesOfType(context, ct);
+    const motifs = normalizeMotifList(params.motifs, new Set(context.labels));
+    return motifCompositionRows(context, ct, motifs, cinds, knnNeighborhood(context, k, maxDist));
+}
+// Compute the composition of motif cell types in the radius-based neighborhoods of center cells.
+// Reference: https://github.com/ShaokunAn/Spatial-Query/blob/9250b61/SpatialQuery/spatial_query.py#L631
+export function motifCompositionDist(context, params) {
+    const { ct, maxDist = 20 } = params;
+    const cinds = getCellIndicesOfType(context, ct);
+    const motifs = normalizeMotifList(params.motifs, new Set(context.labels));
+    return motifCompositionRows(context, ct, motifs, cinds, radiusNeighborhood(context, maxDist));
+}
+//# sourceMappingURL=single-fov.js.map

package/dist/single-fov.js.map

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package/dist/stats.d.ts

@@ -0,0 +1,25 @@
+export declare function roundHalfEven(x: number): number;
+export declare function hypergeom(M: number, n: number, N: number): {
+    mean(): number;
+    sf(k: number): number;
+};
+export declare function normSf(z: number): number;
+export declare function mean(values: number[]): number;
+export declare function median(values: number[]): number;
+export declare function rankAverage(values: number[]): number[];
+export declare function mannWhitneyU(x: number[], y: number[]): {
+    statistic: number;
+    pValue: number;
+};
+export declare function fdrCorrection(pvals: number[], alpha?: number): {
+    rejected: boolean[];
+    adjusted: number[];
+};
+type FdrCorrectable = {
+    pValue: number;
+    adjPValue?: number;
+    ifSignificant?: boolean;
+};
+export declare function applyFdrCorrection<T extends FdrCorrectable>(results: T[], alpha?: number): T[];
+export {};
+//# sourceMappingURL=stats.d.ts.map

package/dist/stats.d.ts.map

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