Example of TnT Genome that shows genes and transcripts in the same track, but transcripts only for a specific gene. This is done by getting the default data retriever for the gene track (which is a promise) and set a new retriever that chains the original one with a function that retrieves all the transcripts (exons, etc) only for the specific gene (PTEN in this case).
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January 12, 2016 16:45
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Genes and transcripts
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| <!DOCTYPE html> | |
| <head> | |
| <link rel="stylesheet" href="http://tntvis.github.io/tnt.genome/build/tnt.genome.css" type="text/css" /> | |
| <style> | |
| #mydiv { | |
| margin-top: 50px; | |
| } | |
| </style> | |
| <script src="http://d3js.org/d3.v3.min.js"></script> | |
| <script src="http://tntvis.github.io/tnt.genome/build/tnt.genome.min.js"></script> | |
| <script src="render.js"></script> | |
| </head> | |
| <body> | |
| <div id="mydiv"></div> | |
| <script> | |
| render(document.getElementById("mydiv")); | |
| </script> | |
| </body> |
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| var thisGene = "PTEN"; | |
| var render = function (div) { | |
| var mixed_track = tnt.board.track() | |
| .height(200) | |
| .color("#EEEFFF") | |
| .display(tnt.board.track.feature.genome.transcript() | |
| .color (function (t) { | |
| if (t.isGene) { | |
| return "#005588"; | |
| } | |
| return "red"; | |
| }) | |
| .on("click", function (d) { | |
| console.log(d); | |
| }) | |
| ); | |
| var mixed_data = tnt.board.track.data.genome.gene(); | |
| var eRest = tnt.board.track.data.genome.ensembl; | |
| var gene_updater = mixed_data.retriever(); | |
| mixed_data.retriever (function (loc) { | |
| return gene_updater.call(mixed_track, loc) | |
| .then (function (genes) { // genes | |
| for (var i=0; i<genes.length; i++) { | |
| genes[i].key = genes[i].id; | |
| genes[i].isGene = true; | |
| genes[i].exons = [{ | |
| start: genes[i].start, | |
| end: genes[i].end, | |
| coding: true, | |
| offset: 0, | |
| isGene: true | |
| }]; | |
| } | |
| var url = eRest.url() | |
| .endpoint("xrefs/symbol/:species/:symbol") | |
| .parameters({ | |
| species: "human", | |
| symbol: thisGene | |
| }); | |
| return eRest.call(url) | |
| .then (function (resp) { | |
| var ensId = resp.body[0].id; | |
| return ensId; | |
| }) | |
| .then (function (ensId) { | |
| var url = eRest.url() | |
| .endpoint("lookup/id/:id") | |
| .parameters({ | |
| id: ensId, | |
| expand: true | |
| }); | |
| return eRest.call(url); | |
| }) | |
| .then (function (resp) { // transcripts + exons | |
| var g = resp.body; | |
| var tss = tnt.board.track.data.genome.transcript().gene2Transcripts(g); | |
| genes = genes.concat(tss); | |
| return genes; | |
| }); | |
| }); | |
| }); | |
| mixed_track | |
| .data(mixed_data); | |
| var genome = tnt.board.genome().species("human").gene(thisGene).width(950); | |
| genome(div); | |
| genome | |
| .zoom_in(100) | |
| .add_track(mixed_track); | |
| genome.start(); | |
| }; |
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