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README.md

Taxonium component

This React component allows phylogenetic trees of up to millions of nodes to be efficiently viewed in the browser.

You can try out Taxonium at taxonium.org.

You can also find fuller documentation for the component and how to embed it in your own site.

Getting started

Here's an example of how to set up the source data and use the Taxonium component in React and basic HTML.

First, set up the source data in JavaScript:

const nwk = `((A:0.1,B:0.2):0.3,(C:0.4,D:0.5):0.6);`;

const metadata_text = `Node,Name,Species
A,Bob,Cow
B,Jim,Cow
C,Joe,Fish
D,John,Fish`;

// Metadata is optional
const metadata = {
  filename: "test.csv",
  data: metadata_text,
  status: "loaded",
  filetype: "meta_csv",
};

const sourceData = {
  status: "loaded",
  filename: "test.nwk",
  data: nwk,
  filetype: "nwk",
  metadata: metadata,
};

In React, you can use the Taxonium component as follows:

yarn add taxonium-component
# or npm install  taxonium-component
import Taxonium from "taxonium-component";

const App = () => {
  return <Taxonium sourceData={sourceData} />;
};

If you're working with basic HTML, you can include the Taxonium component using a script tag:

<body>
  <div id="root"></div>

  <!-- Include peer dependencies -->
  <script src="https://unpkg.com/react@17/umd/react.production.min.js"></script>
  <script src="https://unpkg.com/react-dom@17/umd/react-dom.production.min.js"></script>

  <!-- Include Taxonium Component -->
  <script src="https://unpkg.com/taxonium-component"></script>

  <script>
    // Source data code from above
  </script>

  <script>
    ReactDOM.render(
      React.createElement(Taxonium, { sourceData: sourceData }),
      document.getElementById("root")
    );
  </script>
</body>

Developing the package

yarn install
yarn storybook