Expression Atlas Heatmap

Visualization of baseline, proteomics baseline and differential gene expression experiments for Expression Atlas.

It has four basic visualizations:

• Multiexperiment: collapses several baseline tissue experiments into a single table
• Baseline: displays a single RNA-seq baseline expression experiment
• Proteomics baseline: displays a single proteomics baseline expression experiment
• Differential: displays a single differential expression experiment

Visualizations optionally include, where available, an anatomogram to the left of the table.

Atlas Widget

The heatmap can be included as a widget in your website. Please visit the demo showcase page.

What you need

You must add the following to your environment:

<link rel="stylesheet" type="text/css"
href="https://www.ebi.ac.uk/gxa/resources/css/customized-bootstrap-3.3.5.css"/>

If you already use your own flavour of Bootstrap, then you can remove the styles link tags and the widget will integrate smoothly in your environment.

Are you targetting ES5, IE11 or Safari? Include these polyfills for babel-polyfill and whatwg-fetch:

<script language="JavaScript" type="text/javascript"
src="https://www.ebi.ac.uk/gxa/resources/js/lib/babel-polyfill.min.js"></script>
<script language="JavaScript" type="text/javascript"
src="https://www.ebi.ac.uk/gxa/resources/js/lib/fetch-polyfill.min.js"></script>

Then include our widget and the vendor bundle:

<script language="JavaScript" type="text/javascript"
src="https://www.ebi.ac.uk/gxa/resources/js-bundles/vendorCommons.bundle.js"></script>
<script language="JavaScript" type="text/javascript"
src="https://www.ebi.ac.uk/gxa/resources/js-bundles/expressionAtlasHeatmapHighcharts.bundle.js"></script>

Invoking the widget

You need to call the render method on the exposed global variable:

expressionAtlasHeatmapHighcharts.render({
    query: {
      gene: "ASPM"
    },
    isMultiExperiment: true,
    target: "heatmapContainer"
});

Tell us about any problems by raising an issue in this repository.

Building from source

npm install @ebi-gene-expression-group/expression-atlas-heatmap-highcharts --save

You can use it as a React component:

import ExpressionAtlasHeatmap from '@ebi-gene-expression-group/expression-atlas-heatmap-highcharts'
...
ReactDom.render(<ExpressionAtlasHeatmap .../>, 'id-of-dom-element')

Or mount it on a DOM node if you’re not using the React framework:

import { render as expressionAtlasHeatmapRender } from '@ebi-gene-expression-group/expression-atlas-heatmap-highcharts'
...
expressionAtlasHeatmapRender({...})

For all the options available visit the examples showcase.

Notes for developers

The authoritative docs are the code itself, here is the main function: here

Stay in touch

Besides raising an issue in GitHub, another means of communication with the Expression Atlas development team is the following mailing list: https://listserver.ebi.ac.uk/mailman/listinfo/atlas-widget

It is intended for all developers who integrate the heatmap (we informally refer to it as “the widget”) in their services.

The mailing list is the best way to be informed of official releases of Expression Atlas which are always accompanied by a new supported release of the widget. We also announce new features and (sometimes breaking) changes. We use it also as a channel to make pre-release versions available so that third party services can test the heatmap prior to an Expression Atlas release.

Licence

Source code is licensed under the Apache License, Version 2.0. This does not include the dependencies used by this package, which can be found in the file package.json, and they are covered by the license specified by the corresponding author. This licence extends also to transpiled code as produced by Webpack, Babel or similar tools.

When including the widget on your website, please keep the attribution footer linking to the results in Expression Atlas.

All copyrightable material is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) as detailed in Expression Atlas licence page.

Last updated on 23rd of November, 2017.