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Visualisation JavaScript library for Homologous Genes
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README.md

README.md

aequatus.js

Visualisation JavaScript library for Homologous Genes

Usage

Aequatus.js is a visualisation JavaScript library for Homologous Genes, easy to integrate with existing web services.

To use aequatus.js in your webservice use following simple snippet.

var syntenic_data = json;
init(syntenic_data, "#settings_div", "#filter", "#sliderfilter");
drawTree(syntenic_data.tree, "#gene_tree", popup);

where settings_div, filter_div and sliderfilter are ids for the divs to hold various controls, filter options and slider; and popup is a callback for JavaScript function when clicked on any gene.

An example popup is included in the demo.

Functions:

changeReference(new_gene_id, new_protein_id)

It is used to change reference gene in showing gene families.

Data Format

An Example dataset is provided in the demo/data directory.

snapshot:

{
  "ref":<ref gene id>,
  "protein_id":<ref protein id>,
  "tree":<genetree in JSON>
  "member":<JSON formatted genes array>
}

In which genetree and each gene information can be downloaded from Ensembl using REST API.

  1. Ensembl REST for genetree: http://rest.ensembl.org/documentation/info/genetree
  2. Ensembl REST for gene: http://rest.ensembl.org/documentation/info/lookup

License

aequatus.js is free software: you can redistribute it and/or modify it under the terms of the GMITL License.

aequatus.js is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Project contacts:

© 2015 - 2017. Earlham Institute, Norwich, UK

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