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Using Chromoscope in Different Workflows

There are several ways to use Chromoscope visualizations in different analysis workflows other than directly using the online instance, https://chromoscope.bio/app/. One way is to use the exported Gosling specification and the other is to use Chromoscope Python Package.

tip

To test the following examples of using a customized spec, you can use the spec below.

https://gist.githubusercontent.com/sehilyi/3fa443a629ea924c8b03e58d102c2860/raw/66f8f2a50de44cdb11f433fed0b022a2392f3d19/chromoscope-spec.json

Using Gosling Spec in Online Editor​

Gosling supports an online editor (https://gosling.js.org) where you can copy and paste your exported JSON specification directly on the webpage without any installation.

image
Figure. An example of using Chromoscope's circular visualization in Gosling Online Editor (https://gosling.js.org).

Using Gosling Spec in JavaScript​

You can build a web application using JavaScript (or TypeScript) with React. There is an example GitHub repository (https://github.com/gosling-lang/gosling-react-example) where you can clone the source code and adopt it for your use case.

import { GoslingComponent } from "gosling.js";
import spec from './your-gosling-spec.json'; // customized spec in another file

function App() {
  return (
    <GoslingComponent
      // Gosling specification
      spec={spec}
      // ...
    />
  );
}

Using Gosling Spec in Python Notebooks​

You can use the Gos Python package to use Chromoscope visualization in the computational notebooks, such as Jupyter Notebooks/Labs or Google Colab.

This can be helpful if you understand the grammar of Gosling and want to customize the Chromoscope visualization by editing the exported Gosling spec.

# Install gosling in your python environment
!pip install gosling

# Import gos
import gosling as gos

spec = # Get your spec

# Visualize it using gos
gos.View.from_dict(spec)
image
Figure. An example of using Chromoscope's circular visualization in Google Colab.

Using Chromoscope Python Package​

We also offer a Chromoscope Python Pakcage where you can load Chromoscope directly in the Python notebooks. The main advantage is that you can use local files in your computer without setting up a file server. Please refer to the corresponding documentation.