Getting Started¶
GenomeSpy is a visualization toolkit for genomic data. More specifically, it is a JavaScript library that can be used to create interactive visualizations of genomic data in web browsers. To visualize data with GenomeSpy, you need to:
- Have some data to be visualized
- Write or find a visualization specification that describes how the data should be visualized
- Embed GenomeSpy into a web page and initialize it with the specification and the data
- Open the web page with your web browser
However, there are three ways to get quickly started with GenomeSpy visualizations: the Playground app, Observable notebooks, and embedding GenomeSpy on HTML pages. More advanced users can use GenomeSpy as a visualization library in web applications.
Playground¶
The easiest way to try out GenomeSpy is the Playground app, which allows you to experiment with different visualization specifications directly in your web browser. You can load data from publicly accessible web servers or from your computer. The app is still rudimentary and does not support saving or sharing visualizations.
Observable notebooks¶
You can embed GenomeSpy into an Observable notebook. Please check the GenomeSpy collection for usage examples.
Local or remote web server¶
For more serious work, you should use the GenomeSpy JavaScript library to create a web page for the visualization:
- Create an HTML document (web page) by using the example below
- Place the visualization spec and your data files into the same directory as the HTML document
- Copy them onto a remote web server or start a local web server in the directory
Local web server¶
Python comes with an HTTP server module that can be started from command line:
python3 -m http.server --bind 127.0.0.1
By default, it serves files from the current working directory. See Python's documentation for details.
HTML template¶
The templates below load the GenomeSpy JavaScript library from a content delivery network. Because the specification schema and the JavaScript API are not yet 100% stable, it is recommended to use a specific version.
The embed
function initializes a visualization into the HTML element given as
the first parameter using the specification given as the second parameter. The
function returns a promise that resolves into an object that provides the
current public API. For deails, see the API Documentation.
Check the latest version!
The versions in the examples below may be slightly out of date. The current version is:
Load the spec from a file¶
This template loads the spec from a separate spec.json
file.
<!DOCTYPE html>
<html>
<head>
<title>GenomeSpy</title>
</head>
<body>
<script
type="text/javascript"
src="https://cdn.jsdelivr.net/npm/@genome-spy/core@0.37.x"
></script>
<script>
genomeSpyEmbed.embed(document.body, "spec.json", {});
</script>
</body>
</html>
Embed the spec in the HTML document¶
You can alternatively provide the specification as a JavaScript object.
<!DOCTYPE html>
<html>
<head>
<title>GenomeSpy</title>
</head>
<body>
<script
type="text/javascript"
src="https://cdn.jsdelivr.net/npm/@genome-spy/core@0.37.x"
></script>
<script>
const spec = {
data: {
sequence: { start: 0, stop: 6.284, step: 0.39269908169, as: "x" },
},
transform: [{ type: "formula", expr: "sin(datum.x)", as: "sin" }],
mark: "point",
encoding: {
x: { field: "x", type: "quantitative" },
y: { field: "sin", type: "quantitative" },
},
};
genomeSpyEmbed.embed(document.body, spec, {});
</script>
</body>
</html>
Genomespy.app website examples¶
The examples on the genomespy.app main page are stored in the website-examples GitHub repository. You can clone the repository and launch the examples locally for further experimentation.
Using GenomeSpy as a visualization library in web applications¶
The @genome-spy/core NPM package contains a bundled library that can be used on web pages as shown in the examples above. In addition, it contains the source code in ESM format, allowing use with bundlers such as Vite and Webpack. For examples of such use, see:
- The embed-examples package contains examples of embedding GenomeSpy in web applications and using the API.
- SegmentModel Spy is an example of a complete web application that uses GenomeSpy for visualization.