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Feat/anndata plugin support other table backend #88

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444ec2e
feat!: anndata plugin support for csv, json, parquet table backends
LucaAnce Apr 29, 2026
21a1ab3
fix: numerical values. handle BigInt values from zarr int64 and parqu…
LucaAnce May 5, 2026
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13 changes: 8 additions & 5 deletions anndata-zarr/package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,9 @@
"type": "module",
"main": "dist/biongff-anndata-zarr.cjs.js",
"module": "dist/biongff-anndata-zarr.es.js",
"files": ["dist"],
"files": [
"dist"
],
"exports": {
".": {
"import": "./dist/biongff-anndata-zarr.es.js",
Expand All @@ -23,17 +25,18 @@
},
"dependencies": {
"@tanstack/react-query": "^5.85.3",
"hyparquet": "^1.25.6",
"lodash": "^4.17.21",
"react-window": "^2.0.2",
"zarrita": "0.5.0"
},
"peerDependencies": {
"react": "^18.2.0",
"react-dom": "^18.2.0",
"@emotion/react": "^11.14.0",
"@emotion/styled": "^11.14.1",
"@mui/icons-material": "^7.2.0",
"@mui/material": "^7.2.0",
"@emotion/react": "^11.14.0",
"@emotion/styled": "^11.14.1"
"react": "^18.2.0",
"react-dom": "^18.2.0"
},
"devDependencies": {
"@vitejs/plugin-react": "^4.3.3",
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102 changes: 79 additions & 23 deletions anndata-zarr/src/hooks.js
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Original file line number Diff line number Diff line change
Expand Up @@ -5,27 +5,48 @@ import _ from "lodash";

import { COLORSCALES } from "./constants/colorscales";
import { fetchDataFromZarr, getColors, getObs, getVarNames, getZarrPath } from "./utils";
import {
getTableData,
getFeatureNamesFromTable,
getObsFromTable,
getFeatureDataFromTable,
getColumnDataFromTable,
} from "./table-loader";

const getAnndataColors = async (url, matrixProps, colorProps) => {
let zarrData;
try {
const zarrPath = await getZarrPath(url, matrixProps);
zarrData = await fetchDataFromZarr(zarrPath.url, zarrPath.path, zarrPath.s);
} catch (error) {
console.error(error);
return null;
// ---------------------------------------------------------------------------
// Backend-aware data fetching functions
// ---------------------------------------------------------------------------

async function getFeatureNames(url, namesCol) {
const { meta, data } = await getTableData(url);
if (meta.backend === "anndata") {
return getVarNames(url, namesCol);
}
if (!zarrData) return null;
return getFeatureNamesFromTable(data, meta.indexKey, meta);
}

const { categories } = zarrData;
async function getObsColumns(url) {
const { meta, data } = await getTableData(url);
if (meta.backend === "anndata") {
return getObs(url);
}
return getObsFromTable(data, meta.indexKey, meta);
}

const max = categories ? categories.length - 1 : colorProps?.max || _.max(zarrData.data);
const min = categories ? 0 : colorProps?.min || _.min(zarrData.data);
function computeColorResult(columnData, colorProps) {
if (!columnData) return null;
const { categories } = columnData;
// Convert BigInt data (from int64 zarr arrays or parquet) to Number
let data = columnData.data;
if (data?.length > 0 && typeof data[0] === "bigint") {
data = Array.from(data, Number);
}
const max = categories ? categories.length - 1 : Number(colorProps?.max || _.max(data));
const min = categories ? 0 : Number(colorProps?.min || _.min(data));
const colorscale = categories ? COLORSCALES.Accent : colorProps?.colorscale;

return {
colors: getColors({
data: zarrData.data,
data,
max,
min,
colorProps: { ...colorProps, colorscale },
Expand All @@ -36,16 +57,51 @@ const getAnndataColors = async (url, matrixProps, colorProps) => {
...(categories ? { categories } : {}),
colorscale,
};
};
}

async function getColorData(url, matrixProps, colorProps) {
const { meta, data } = await getTableData(url);

let columnData;
if (meta.backend === "anndata") {
try {
const zarrPath = await getZarrPath(url, matrixProps);
columnData = await fetchDataFromZarr(zarrPath.url, zarrPath.path, zarrPath.s);
} catch (error) {
console.error(error);
return null;
}
} else {
const { feature, obs } = matrixProps || {};
try {
if (feature?.index !== undefined && feature?.index !== null) {
columnData = getFeatureDataFromTable(data, feature.index, meta.indexKey, meta);
} else if (feature?.name) {
columnData = getColumnDataFromTable(data, feature.name);
} else if (obs?.col) {
columnData = getColumnDataFromTable(data, obs.col);
}
} catch (error) {
console.error(error);
return null;
}
}

return computeColorResult(columnData, colorProps);
}

// ---------------------------------------------------------------------------
// Hooks
// ---------------------------------------------------------------------------

export const useAnndataColors = (adata = { url: null }, opts = {}) => {
const {
data = null,
isLoading = false,
serverError = null,
} = useQuery({
queryKey: ["anndataColor", adata.url, adata.matrixProps, adata.colorProps],
queryFn: () => getAnndataColors(adata.url, adata.matrixProps, adata.colorProps),
queryKey: ["tableColor", adata.url, adata.matrixProps, adata.colorProps],
queryFn: () => getColorData(adata.url, adata.matrixProps, adata.colorProps),
...opts,
});

Expand All @@ -67,8 +123,8 @@ export const useAnndatasColors = (adatas = [], opts = {}) => {
serverError = null,
} = useQueries({
queries: adatas.map(({ url, matrixProps, colorProps }) => ({
queryKey: ["anndataColor", url, matrixProps, colorProps],
queryFn: () => getAnndataColors(url, matrixProps, colorProps),
queryKey: ["tableColor", url, matrixProps, colorProps],
queryFn: () => getColorData(url, matrixProps, colorProps),
})),
...opts,
combine,
Expand All @@ -83,8 +139,8 @@ export const useAnndataFeatures = (adata = { url: null, namesCol: null }) => {
isLoading = false,
serverError = null,
} = useQuery({
queryKey: ["anndataFeatures", adata.url, adata.namesCol],
queryFn: () => getVarNames(adata.url, adata.namesCol),
queryKey: ["tableFeatures", adata.url, adata.namesCol],
queryFn: () => getFeatureNames(adata.url, adata.namesCol),
});

return { data, isLoading, serverError };
Expand All @@ -96,8 +152,8 @@ export const useAnndataObs = (adata = { url: null }) => {
isLoading = false,
serverError = null,
} = useQuery({
queryKey: ["anndataObs", adata.url],
queryFn: () => getObs(adata.url),
queryKey: ["tableObs", adata.url],
queryFn: () => getObsColumns(adata.url),
});

return { data, isLoading, serverError };
Expand Down
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