Genome browser for phamerator.org
forked from scresawn's block: genome browser
forked from grybnicky's block: genome browser
forked from grybnicky's block: genome browser with GC
forked from jpnoll's block: genome browser with GC
forked from jpnoll's block: genome browser
forked from jpnoll's block: genome browser
| [{ | |
| "name": 1, | |
| "pham": 7, | |
| "sequence": "ATGCTACGTAGCTACGTACGATCGTACGATCGATCGTACG", | |
| "start": 50, | |
| "stop": 2000, | |
| "direction": "forward" | |
| }, | |
| { | |
| "name": 2, | |
| "pham": 201, | |
| "sequence": "GACTGACTGACTAGCTGACTGATCGTACTCGAT", | |
| "start": 2150, | |
| "stop": 2900, | |
| "direction": "reverse" | |
| }, | |
| { | |
| "name": 3, | |
| "pham": 90, | |
| "sequence": "ATCGTACGTACGTACGTACGATCGTACGATCGCGCGCGCGGCGCATCGATCGATCGTACTA", | |
| "start": 3000, | |
| "stop": 4550, | |
| "direction": "reverse" | |
| }, | |
| { | |
| "name": 4, | |
| "pham": 3752, | |
| "sequence": "TTCTAGTCGATCGTACGTGTACGTGCATTATTGATGCTATATATCGTATATACGTA", | |
| "start": 4700, | |
| "stop": 7550, | |
| "direction": "forward" | |
| } | |
| ] |
| <!DOCTYPE html> | |
| <head> | |
| <meta charset="utf-8"> | |
| <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script> | |
| <link rel="stylesheet" type="text/css" href="http://fonts.googleapis.com/css?family=Roboto+Slab:400,100,300,700"> | |
| <link rel="stylesheet" type="text/css" href="http://fonts.googleapis.com/css?family=Roboto:400,100,100italic,300,300italic,400italic,500,500italic,700,700italic,900,900italic"> | |
| </head> | |
| <body> | |
| <script> | |
| // Feel free to change or delete any of the code you see! | |
| var genomelength = 7800; | |
| var tickMarks = {thousand: [], fivehundred: [], onehundred: []}; | |
| var genome_positions = []; | |
| for (var i = 1; i <= genomelength; i++) { | |
| genome_positions.push(i); | |
| } | |
| genome_positions.forEach(function(currentValue, index, myArray){ | |
| if (currentValue % 1000 === 0) { | |
| tickMarks.thousand.push(currentValue); | |
| } | |
| else if (currentValue % 500 === 0) { | |
| tickMarks.fivehundred.push(currentValue); | |
| } | |
| else if (currentValue % 100 === 0) { | |
| tickMarks.onehundred.push(currentValue); | |
| } | |
| }); | |
| var svg = d3.select("body").append("svg").attr({height: 500,width: genomelength/10}); | |
| svg.append("rect") | |
| .attr({x: 0, y: 100, width: genomelength/10, height: 30}) | |
| .style({"stroke-width": "2px", "fill": "white", "stroke": "black"}) | |
| .attr("stroke-opacity", 0) | |
| .transition().duration(1000) | |
| .attr("stroke-opacity", 1); | |
| d3.json("genes.json.txt", function(error, json) { | |
| if (error) return console.warn(error); | |
| var genes = svg.selectAll(".genes") | |
| .data(json) | |
| .enter() | |
| .append("g"); | |
| genes.append("rect") | |
| .attr("fill", function (d) { | |
| if (d.direction == "forward") { | |
| return "green"; | |
| } | |
| else if (d.direction == "reverse") { | |
| return "red"; | |
| } | |
| else { | |
| return "black"; | |
| } | |
| }) | |
| .on("mouseover", function(){ | |
| d3.select(this) | |
| .style("fill","yellow") | |
| }) | |
| .on("mouseout", function(){ | |
| d3.select(this) | |
| .style("fill", function (d) { | |
| if (d.direction == "forward") { | |
| return "green"; | |
| } | |
| else if (d.direction == "reverse") { | |
| return "red"; | |
| } | |
| else { | |
| return "black"; | |
| } | |
| })}) | |
| .attr("y", function (d) { | |
| if (d.direction == "forward") { | |
| if (d.name % 2 === 0) { | |
| return 70; | |
| } | |
| else { return 40;} | |
| } | |
| else if (d.direction == "reverse") { | |
| if (d.name % 2 === 0) { | |
| return 160; | |
| } | |
| else { return 130; } | |
| } | |
| }) | |
| .attr("x", function (d) { | |
| if (d.direction === "forward") { | |
| return (0 - ((d.stop-d.start)/10)) - 2; | |
| } | |
| else if (d.direction === "reverse") { | |
| return (genomelength/10) + 2; | |
| } | |
| }) | |
| .attr("height", function (d) {return 30;}) | |
| .attr("width", function (d) { return (d.stop-d.start)/10; }) | |
| .style({"stroke":"black", "stroke-width": "2px"}) | |
| .transition().delay(1000).duration(1500).attr("x", function (d) { return d.start/10; }); | |
| genes.append("text") // GC | |
| .attr("x", function(d) { return ((d.start + d.stop)/2)/10;}) | |
| .attr("y", function (d) { | |
| if (d.direction == "forward") { | |
| if (d.name % 2 === 0) { | |
| return 90; | |
| } | |
| else { return 60;} | |
| } | |
| else if (d.direction == "reverse") { | |
| if (d.name % 2 === 0) { | |
| return 180; | |
| } | |
| else { return 150;} | |
| } | |
| }) | |
| .style({"text-anchor": "middle", "fill": "black"}) | |
| .attr("font-family", "sans-serif") | |
| .text(function(d) { | |
| return ((((d.sequence.match(/G/gi).length)+(d.sequence.match(/C/gi).length))/(d.sequence.length))*100).toPrecision(3)+"%"; | |
| }) | |
| .attr("fill-opacity", 0) | |
| .transition().delay(2000).duration(1500) | |
| .attr("fill-opacity", 1); | |
| genes.append("text") // pham name | |
| .attr("x", function(d) { | |
| return ((d.start + d.stop)/2)/10; | |
| }) | |
| .attr("y", function (d) { | |
| if (d.direction == "forward") { | |
| if (d.name % 2 === 0) { | |
| return 60; | |
| } | |
| else { return 30;} | |
| } | |
| else if (d.direction == "reverse") { | |
| if (d.name % 2 === 0) { | |
| return 210; | |
| } | |
| else { return 180;} | |
| } | |
| }) | |
| .style({"text-anchor": "middle", "fill": "black"}) | |
| .attr("font-family", "sans-serif") | |
| .text(function(d) { | |
| return d.pham | |
| }) | |
| .attr("fill-opacity", 0) | |
| .transition().delay(3500).duration(1500) | |
| .attr("fill-opacity", 1); | |
| }); | |
| var group = svg.selectAll(".thousandticks") | |
| .data(tickMarks.thousand) | |
| .enter() | |
| .append("g"); | |
| group.append("rect") | |
| .style({"fill": "black"}) | |
| //.attr({x: 0, y: 100, width: "1px", height: 30}) | |
| .attr({x: function (d) { return d/10; }, y: 100, width: "1px", height: 30}) | |
| .attr({"fill-opacity": 0}) | |
| .transition().duration(1500) | |
| .attr({"fill-opacity": 1}); | |
| //.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; }); | |
| group.append("text") | |
| .attr("x", function(d) {return (d/10) + 3;}) | |
| .attr("y", (90) + 22) | |
| .attr("font-family", "sans-serif") | |
| .attr("font-size", "14px") | |
| .attr("fill", "green") | |
| .style("text-anchor", "start") | |
| .text(function(d) { return d/1000; }) | |
| .attr({"fill-opacity": 0}) | |
| .transition().duration(1500) | |
| .attr({"fill-opacity": 1}); | |
| var group2 = svg.selectAll(".fivehundredticks") | |
| .data(tickMarks.fivehundred) | |
| .enter() | |
| .append("g"); | |
| group2.append("rect") | |
| .style({"fill": "black"}) | |
| .attr({x: function(d) {return d/10;}, y: 100, width: "1px", height: 15}) | |
| .attr({"fill-opacity": 0}) | |
| .transition().duration(1500) | |
| .attr({"fill-opacity": 1}); | |
| //.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; }); | |
| var group3 = svg.selectAll(".onehundredticks") | |
| .data(tickMarks.onehundred) | |
| .enter() | |
| .append("g"); | |
| group3.append("rect") | |
| .style({"fill": "black"}) | |
| .attr({x: function (d) { return d/10; }, y: 115, width: "1px", height: 15}) | |
| .attr("fill-opacity", 0) | |
| .transition().duration(1500) | |
| .attr("fill-opacity", 1); | |
| //.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; }); | |
| </script> | |
| </body> |