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<!DOCTYPE html> |
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<head> |
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<meta charset="utf-8"> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script> |
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<script src="http://d3js.org/d3.v3.min.js"></script> |
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<link rel="stylesheet" type="text/css" href="http://fonts.googleapis.com/css?family=Roboto+Slab:400,100,300,700"> |
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<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"> |
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</head> |
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<body> |
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<style> |
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/* set the CSS */ |
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div.tooltip { |
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position: absolute; |
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text-align: center; |
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width: 60px; |
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height: 60px; |
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padding: 2px; |
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font: 12px ariel; |
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background: lavender; |
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border: 0px; |
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border-radius: 8px; |
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pointer-events: none; |
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} |
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</style> |
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<script> |
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var svg = d3.select("body").append("svg").attr("height", 1000); |
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//new gene comparison |
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d3.json("test.json", function(error, json) { |
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//console.log(json); |
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// if (error) return console.warn(error); |
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//console.log(hsps); |
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var data = function(hsps) { |
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//console.log(Array.isArray(hsps)); |
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var paths = Array(); |
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hsps.forEach(function(value, index, myArray) { |
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//console.log(value); |
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var dataset = Array(); |
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dataset.push({x: value.query_from/10, y: 130}); |
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dataset.push({x: value.query_to/10, y: 130}); |
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dataset.push({x: value.hit_to/10, y: 325}); |
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dataset.push({x: value.hit_from/10, y: 325}); |
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paths.push(dataset); |
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}); |
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//console.log(dataset); |
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return paths; |
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} |
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var hsps = json.BlastOutput2[0].report.results.bl2seq[0].hits[0].hsps; |
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//console.log(hsps); |
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/*var hsps = svg.selectAll(".hsps") |
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.data(json.BlastOutput2[0].report.results.bl2seq[0].hits[0].hsps);*/ |
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pathset = data(hsps); |
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var hsps = svg.selectAll(".hsps") |
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.data(pathset); |
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var d3line2 = d3.svg.line() |
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.x(function(d) { return d.x; }) |
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.y(function(d) { return d.y; }) |
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.interpolate("linear-closed"); |
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hsps.enter() |
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.append("svg:path") |
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.style("fill-opacity", 0) |
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.style("stroke-width", 0) |
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.attr("d", function(d) { console.log(d); return d3line2(d);}) |
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.transition() |
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.duration(3000) |
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.delay(4000) |
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.style("stroke-width", 1) |
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.style("stroke", "black") |
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.style("fill", "red") |
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.style("fill-opacity", 0.5) |
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hsps.on("mouseover", function(){ |
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d3.select(this).style("fill", "pink"); |
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return tooltip.style("visibility", "visible"); |
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}) |
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.on("mouseout", function(){d3.select(this).style("fill", "red");}) |
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/*hsps .on("mouseover", function(){return tooltip.style("visibility", "visible");})*/ |
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.on("mousemove", function(){return tooltip.style("top", (event.pageY-10)+"px").style("left",(event.pageX+10)+"px");}) |
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.on("mouseout", function(){ |
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d3.select(this).style("fill", "red"); |
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return tooltip.style("visibility", "hidden"); |
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}) |
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var tooltip = d3.select("body") |
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.append("div") |
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.style("z-index", "10") |
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.style("visibility", "hidden") |
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.text("evalue") |
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.style("background","lightcyan") |
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.style("width","50px") |
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.style("height", "30px") |
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.style("text-align", "center") |
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.style("position", "absolute") |
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.style("padding", "2px") |
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.style("font", "ariel") |
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.style("border-radius","8px"); |
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}); |
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d3.json("genes.json.txt", function(error, json) { |
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if (error) return console.warn(error); |
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//console.log(json); |
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svg.attr("width", function (d) { |
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return d3.max(json, function(d) { |
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return d.genomelength/10; |
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}) |
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}); |
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// Define the div for the tooltip |
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var div = d3.select("body").append("div") |
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.attr("class", "tooltip") |
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.style("opacity", 0); |
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var phage = svg.selectAll(".genomes") |
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.data(json) |
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.enter() |
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.append("g"); |
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phage.attr("transform", function(d, i) { return "translate(0," + (100 + (i*225)) + ")"; }); |
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phage.append("rect") // background for ruler |
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.attr({x: 0, y: 0, width: function(d) { return d.genomelength/10; }, height: 30}) |
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.style({"stroke-width": "2px", "fill": "white", "stroke": "black"}) |
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.attr("stroke-opacity", 0) |
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.transition().duration(1000) |
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.attr("stroke-opacity", 1) |
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; |
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var group = phage.selectAll(".thousandticks") |
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.data(function (d) { |
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ticks = []; |
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genome_positions = d3.range(d.genomelength); |
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genome_positions.forEach(function (currentValue, index, myArray) { |
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if (currentValue % 1000 === 0) { |
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ticks.push(currentValue); |
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} |
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}); |
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return ticks; |
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} |
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) |
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.enter() |
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.append("g"); |
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group.append("rect") |
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.style({"fill": "black"}) |
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//.attr({x: 0, y: 100, width: "1px", height: 30}) |
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.attr({x: function (d) { return d/10; }, y: 0, width: "1px", height: 30}) |
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.attr({"fill-opacity": 0}) |
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.transition().duration(1500) |
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.attr({"fill-opacity": 1}); |
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//.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; }); |
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group.append("text") // kbp label |
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.attr("x", function(d) {return (d/10) + 3;}) |
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.attr("y", 12) |
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.attr("font-family", "ariel") |
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.attr("font-size", "14px") |
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.attr("fill", "black") |
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.style("text-anchor", "start") |
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.text(function(d) { return d/1000; }) |
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.attr({"fill-opacity": 0}) |
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.transition().duration(1500) |
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.attr({"fill-opacity": 1}); |
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var group2 = phage.selectAll(".fivehundredticks") |
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.data(function (d) { |
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ticks = []; |
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genome_positions = d3.range(d.genomelength); |
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genome_positions.forEach(function (currentValue, index, myArray) { |
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if (currentValue % 500 === 0 & currentValue % 1000 !== 0) { |
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ticks.push(currentValue); |
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} |
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}) |
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return ticks; |
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}) |
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.enter() |
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.append("g"); |
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group2.append("rect") |
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.style({"fill": "black"}) |
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.attr({x: function(d) {return d/10;}, y: 0, width: "1px", height: 15}) |
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.attr({"fill-opacity": 0}) |
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.transition().duration(1500) |
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.attr({"fill-opacity": 1}); |
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//.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; }); |
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var group3 = phage.selectAll(".onehundredticks") |
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.data(function (d) { |
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ticks = []; |
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genome_positions = d3.range(d.genomelength); |
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genome_positions.forEach(function (currentValue, index, myArray) { |
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if (currentValue % 100 === 0 & currentValue % 1000 !== 0 & currentValue % 500 !== 0) { |
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ticks.push(currentValue); |
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} |
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}) |
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return ticks; |
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}) |
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.enter() |
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.append("g"); |
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group3.append("rect") |
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.style({"fill": "black"}) |
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.attr({x: function (d) { return d/10; }, y: 15, width: "1px", height: 15}) |
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.attr("fill-opacity", 0) |
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.transition().duration(1500) |
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.attr("fill-opacity", 1); |
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gene = phage.selectAll(".genes") |
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.data(function(d, i) { return d.genes;}) |
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.enter() |
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.append("g"); |
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gene.append("rect") |
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.attr("y", function (d) { |
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if (d.direction == "forward") { |
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if (d.name % 2 === 0) { |
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return -70; |
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} |
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else { return -30;} |
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} |
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else if (d.direction == "reverse") { |
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if (d.name % 2 === 0) { |
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return 30; |
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} |
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else { return 60;} |
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} |
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}) |
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.attr("x", function (d) { |
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if (d.direction === "forward") { |
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return (0 - ((d.stop-d.start)/10)) - 2; |
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} |
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else if (d.direction === "reverse") { |
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w = d3.select("svg").style("width"); |
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return w; |
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} |
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}) |
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.attr("height", function (d) {return 30;}) |
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.attr("width", function (d) { return (d.stop-d.start)/10; }) |
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.style({"stroke":"black", "stroke-width": "2px"}) |
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.attr("fill", function (d) { |
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if (d.direction == "forward") { |
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return "aquamarine"; |
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} |
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else if (d.direction == "reverse") { |
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return "lightskyblue"; |
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} |
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else { |
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return "black"; |
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} |
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}) |
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.on("mouseover", function(d) { |
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//console.log(d); |
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div.transition() |
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.duration(500) |
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.style("opacity", .9); |
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div .html("The direction of gene " + d.name + " is " + d.direction) |
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// the text of the tooltip ... |
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.style("left", (d3.event.pageX) + "px") |
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.style("top", (d3.event.pageY - 28) + "px"); |
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}) |
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.on("mouseout", function(d) { |
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div.transition() |
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.duration(500) |
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.style("opacity", 0); |
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}) |
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.transition().delay(1000).duration(1500) |
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.attr("x", function (d) { return d.start/10; }); |
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gene.append("text") // gene name |
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.attr("x", function(d) { return ((d.start + d.stop)/2)/10;}) |
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.attr("y", function (d) { |
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if (d.direction == "forward") { |
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if (d.name % 2 === 0) { // forward and even |
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return -50; |
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} |
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else { return -10;} // forward and odd |
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} |
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else if (d.direction == "reverse") { |
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if (d.name % 2 === 0) { // reverse and even |
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return 50; |
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} |
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else { return 80;} //reverse and odd |
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} |
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}) |
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.style({"text-anchor": "middle", "fill": "black"}) |
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.attr("font-family", "ariel") |
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.text(function(d) {return d.name}) |
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.attr("fill-opacity", 0) |
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.transition().delay(2000).duration(1500) |
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.attr("fill-opacity", 1) |
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; |
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gene.append("text") // pham name |
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.attr("x", function(d) { return ((d.start + d.stop)/2)/10;}) |
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.attr("y", function (d) { |
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if (d.direction == "forward") { |
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if (d.name % 2 === 0) { |
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return -80; |
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} |
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else { return -40;} |
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} |
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else if (d.direction == "reverse") { |
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if (d.name % 2 === 0) { |
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return 80; |
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} |
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else { return 110;} |
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} |
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}) |
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.style({"text-anchor": "middle", "fill": "black"}) |
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.attr("font-family", "ariel") |
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.text(function(d) {return d.pham}) |
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.attr("fill-opacity", 0) |
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.transition().delay(3500).duration(1500) |
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.attr("fill-opacity", 1) |
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; |
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}); |
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</script> |
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<script> |
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</script> |
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</body> |