higlass-zarr-datafetchers

This repository contains plugin data fetchers for loading Zarr-based files in HiGlass. These plugins allow data to be stored in object stores such as S3 (rather than using higlass-server). Plugin data fetchers can be registered using higlass-register.

Installation

yarn add zarr # peer dependency
yarn add higlass-register # helpers for plugin registration
yarn add higlass-zarr-datafetchers

Register plugin data fetchers

import register from "higlass-register";
import { ZarrMultivecDataFetcher } from "higlass-zarr-datafetchers";

register(
    { dataFetcher: ZarrMultivecDataFetcher, config: ZarrMultivecDataFetcher.config },
    { pluginType: "dataFetcher" }
);

Use in a HiGlass view config track definition

List of data fetchers currently implemented:

• zarr-multivec (register with ZarrMultivecDataFetcher)

  • Use this data fetcher with a horizontal-multivec track to visualize multi-sample genome-wide continuous data.

  {
      "type": "horizontal-multivec",
      "uid": "demo-multivec-track",
      "data": {
          "type": "zarr-multivec",
          "url": "//higlass-serverless.s3.amazonaws.com/multivec/Homo_sapiens__AFF4__all.multires.zarr",
      },
  }

  • Alternatively, use this data fetcher with a horizontal-bar track to visualize single-sample genome-wide continuous data (one row of a multi-sample file).

  {
      "type": "horizontal-bar",
      "uid": "demo-bar-track",
      "data": {
          "type": "zarr-multivec",
          "url": "//higlass-serverless.s3.amazonaws.com/multivec/Homo_sapiens__AFF4__all.multires.zarr",
          "row": 0, // specify the index of a row of interest
      },
  }

Develop

Install dependencies

yarn

Run the demo

yarn run start

Build

yarn run build

Conversion resources

Coming soon: higlass-zarr-converters

For the current demo, Zarr files were generated using this script