biojs-vis-exon-intron-map

Generates exon intron map

Usage no npm install needed!

<script type="module">
  import biojsVisExonIntronMap from 'https://cdn.skypack.dev/biojs-vis-exon-intron-map';
</script>

README

biojs-vis-exon-intron-map

Create an exon intron map for alternative spliceforms with decorations

NPM version

exon_intron LOGO

Getting Started in the browser

<script src="js/d3.js"></script>
<script src="js/biojs-vis-exon-intron-map.js"></script>
<link rel="stylesheet" href="css/biojs-vis-exon-intron-map.css">
  • exons are in UPPERCASE and introns in lowercase
  • sequences supplied in fastA format with line break \n after identifier
let myMap = new exonIntronMap(">C10G8.5a\nATGACTCGATTAGGGTGTTGGCTAGCAGTAGCCTTTCTGGTGGCCCTCGCTGGACTCGCAGATGCTGGATCCAACTGTTCAGCAGCCGACGCCACTAGAAACTGCATCGATGGACTTGTTATACCTATTTGgtgaggatttaaactaaaacaaagcttgaat>C10G8.5b\nATGACTCGATTAGGGTGTTGGCTAGCAGTAGCCTTTCTGGTGGCCCTCGCTGGACTCGCAGATGCTGGATCCAACTGTTCAGCAGCCGACGCCACTAGAAACTGCATCGATGGACTTGTTATACCTATTTGgtgaggatttaaactaaaacaaagcttgaatcaaaatttga>C10G8.5c\nATGAAGGAGGGAGAGATCGTTTTTGAAGACAACCAGACTGAgtacatcacctaccaatatcgtttttcttcaactttttttccagAGCTCTTGTTGAAATTGGAATTGTCGATACTGAACAATACGAACGCTCCGACTACTTCTACATCGAGCTTTCCCCACCAATCTGGGCCAAGAAGATGAATGgtgagtatttttggaactatttttttaagtgaaacaacaaaaacgcttctacatatacatatgtgcacattgttaatttcactacaacaacacaacaacaaaaacaatcaattaat");
  • add coordinates to position the spliceforms relative to one another and correctly number the scale
  • Must be supplied in the same order as the sequences
myMap.coords = "5303692,5303692,5307700";
  • label the scale:
myMap.chromosomeName = "Chromosome II";
  • add decorations:
  1. SNP
myMap.snpPoint = 3800;
const Arrow = '\u2192';
myMap.snpText = "ATG" + Arrow + "GTG";
  1. Deletion
myMap.deletion = "1200,1650";
myMap.delName = "ems deletion";
  1. Insertion
myMap.knockinPoint = 5650;
myMap.knockinText =  "GFP CRISPR insert";
myMap.knockinColor = "green";
  1. render the SVG image
myMap.render();

From npm

  • npm install biojs-vis-exon-intron-map

Output

  • Exon intron graphic with lesion decorations in high resolution Scalable Vector Graphics (SVG) format

Example directory

  • sample files are rendered from the examples dir at the BioJS registry
  • note: it takes a minute to render the sample files at BioJS

Contributing

All contributions are welcome.

Support

If you have any problem or suggestion please open an issue here.

License

The MIT License

Copyright (c) 2016, dohalloran

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.