Genome browser for phamerator.org
forked from scresawn's block: genome browser
forked from smith13mr's block: genome browser for final group project
forked from scresawn's block: genome browser for final group project
forked from smith13mr's block: Two tooltips and fade out
forked from scresawn's block: Two tooltips and fade out
xxxxxxxxxx
<head>
<meta charset="utf-8">
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>
<script src="https://d3js.org/d3.v3.min.js"></script>
<link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto+Slab:400,100,300,700">
<link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto:400,100,100italic,300,300italic,400italic,500,500italic,700,700italic,900,900italic">
</head>
<body>
<style>
/* set the CSS */
div.tooltip {
position: absolute;
text-align: center;
width: 60px;
height: 60px;
padding: 2px;
font: 12px Arial;
background: lavender;
border: 0px;
border-radius: 8px;
pointer-events: none;
}
</style>
<script>
var svg = d3.select("body").append("svg").attr("height", 1000);
d3.json("test.json", function(error, json) {
var data = function(hsps) {
var paths = Array();
hsps.forEach(function(value, index, myArray) {
var dataset = Array();
dataset.push({x: value.query_from/10, y: 130, evalue: value.evalue});
dataset.push({x: value.query_to/10, y: 130});
dataset.push({x: value.hit_to/10, y: 325});
dataset.push({x: value.hit_from/10, y: 325});
paths.push(dataset);
});
return paths;
}
var hsps = json.BlastOutput2[0].report.results.bl2seq[0].hits[0].hsps;
pathset = data(hsps);
var hsps = svg.selectAll(".hsps")
.data(pathset);
var d3line2 = d3.svg.line()
.x(function(d) { return d.x; })
.y(function(d) { return d.y; })
.interpolate("linear-closed");
hsps.enter()
.append("svg:path")
.on("mouseover", function(d){
console.log(d);
tooltip.html("e-value: " + d[0].evalue) ;
d3.select(this).style("fill", "pink");
return tooltip.style("visibility", "visible");
})
.style("fill-opacity", 0)
.style("stroke-width", 0)
.attr("d", function(d) { //console.log(d);
return d3line2(d);})
.transition()
.duration(3000)
.delay(4000)
.style("stroke-width", 1)
.style("stroke", "black")
.style("fill", "red")
.style("fill-opacity", 0.5)
hsps.on("mouseout", function(){d3.select(this).style("fill", "red");})
.on("mousemove", function(){return tooltip.style("top", (event.pageY-10)+"px").style("left",(event.pageX+10)+"px");})
.on("mouseout", function(){
d3.select(this).style("fill", "red");
return tooltip.style("visibility", "hidden");
})
var tooltip = d3.select("body")
.append("div")
.style("z-index", "10")
.style("visibility", "hidden")
.style("background","lightcyan")
.style("width","150px")
.style("height", "30px")
.style("text-align", "center")
.style("position", "absolute")
.style("padding", "2px")
.style("font", "ariel")
.style("border-radius","8px");
});
d3.json("genes.json.txt", function(error, json) {
if (error) return console.warn(error);
svg.attr("width", function (d) {
return d3.max(json, function(d) {
return d.genomelength/10;
})
});
// Define the div for the tooltip
var div = d3.select("body").append("div")
.attr("class", "tooltip")
.style("opacity", 0);
var phage = svg.selectAll(".genomes")
.data(json)
.enter()
.append("g");
phage.attr("transform", function(d, i) { return "translate(0," + (100 + (i*225)) + ")"; });
phage.append("rect") // background for ruler
.attr({x: 0, y: 0, width: function(d) { return d.genomelength/10; }, height: 30})
.style({"stroke-width": "2px", "fill": "white", "stroke": "black"})
.attr("stroke-opacity", 0)
.transition().duration(1000)
.attr("stroke-opacity", 1)
;
var group = phage.selectAll(".thousandticks")
.data(function (d) {
ticks = [];
genome_positions = d3.range(d.genomelength);
genome_positions.forEach(function (currentValue, index, myArray) {
if (currentValue % 1000 === 0) {
ticks.push(currentValue);
}
});
return ticks;
}
)
.enter()
.append("g");
group.append("rect")
.style({"fill": "black"})
.attr({x: function (d) { return d/10; }, y: 0, width: "1px", height: 30})
.attr({"fill-opacity": 0})
.transition().duration(1500)
.attr({"fill-opacity": 1});
group.append("text") // kbp label
.attr("x", function(d) {return (d/10) + 3;})
.attr("y", 12)
.attr("font-family", "ariel")
.attr("font-size", "14px")
.attr("fill", "black")
.style("text-anchor", "start")
.text(function(d) { return d/1000; })
.attr({"fill-opacity": 0})
.transition().duration(1500)
.attr({"fill-opacity": 1});
var group2 = phage.selectAll(".fivehundredticks")
.data(function (d) {
ticks = [];
genome_positions = d3.range(d.genomelength);
genome_positions.forEach(function (currentValue, index, myArray) {
if (currentValue % 500 === 0 & currentValue % 1000 !== 0) {
ticks.push(currentValue);
}
})
return ticks;
})
.enter()
.append("g");
group2.append("rect")
.style({"fill": "black"})
.attr({x: function(d) {return d/10;}, y: 0, width: "1px", height: 15})
.attr({"fill-opacity": 0})
.transition().duration(1500)
.attr({"fill-opacity": 1});
var group3 = phage.selectAll(".onehundredticks")
.data(function (d) {
ticks = [];
genome_positions = d3.range(d.genomelength);
genome_positions.forEach(function (currentValue, index, myArray) {
if (currentValue % 100 === 0 & currentValue % 1000 !== 0 & currentValue % 500 !== 0) {
ticks.push(currentValue);
}
})
return ticks;
})
.enter()
.append("g");
group3.append("rect")
.style({"fill": "black"})
.attr({x: function (d) { return d/10; }, y: 15, width: "1px", height: 15})
.attr("fill-opacity", 0)
.transition().duration(1500)
.attr("fill-opacity", 1);
gene = phage.selectAll(".genes")
.data(function(d, i) { return d.genes;})
.enter()
.append("g");
gene.append("rect")
.attr("y", function (d) {
if (d.direction == "forward") {
if (d.name % 2 === 0) {
return -70;
}
else { return -30;}
}
else if (d.direction == "reverse") {
if (d.name % 2 === 0) {
return 30;
}
else { return 60;}
}
})
.attr("x", function (d) {
if (d.direction === "forward") {
return (0 - ((d.stop-d.start)/10)) - 2;
}
else if (d.direction === "reverse") {
w = d3.select("svg").style("width");
return w;
}
})
.attr("height", function (d) {return 30;})
.attr("width", function (d) { return (d.stop-d.start)/10; })
.style({"stroke":"black", "stroke-width": "2px"})
.attr("fill", function (d) {
if (d.direction == "forward") {
return "aquamarine";
}
else if (d.direction == "reverse") {
return "lightskyblue";
}
else {
return "black";
}
})
.on("mouseover", function(d) {
//console.log(d);
div.transition()
.duration(500)
.style("opacity", .9);
div .html(d.protein)
// the text of the tooltip ...
.style("left", (d3.event.pageX) + "px")
.style("top", (d3.event.pageY - 28) + "px");
})
.on("mouseout", function(d) {
div.transition()
.duration(500)
.style("opacity", 0);
})
.transition().delay(1000).duration(1500)
.attr("x", function (d) { return d.start/10; });
gene.append("text") // gene 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) { // forward and even
return -50;
}
else { return -10;} // forward and odd
}
else if (d.direction == "reverse") {
if (d.name % 2 === 0) { // reverse and even
return 50;
}
else { return 80;} //reverse and odd
}
})
.style({"text-anchor": "middle", "fill": "black"})
.attr("font-family", "ariel")
.text(function(d) {return d.name})
.attr("fill-opacity", 0)
.transition().delay(2000).duration(1500)
.attr("fill-opacity", 1)
;
gene.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 -80;
}
else { return -40;}
}
else if (d.direction == "reverse") {
if (d.name % 2 === 0) {
return 80;
}
else { return 110;}
}
})
.style({"text-anchor": "middle", "fill": "black"})
.attr("font-family", "ariel")
.text(function(d) {return d.pham})
.attr("fill-opacity", 0)
.transition().delay(3500).duration(1500)
.attr("fill-opacity", 1)
;
});
</script>
<script>
</script>
</body>
Modified http://d3js.org/d3.v3.min.js to a secure url
https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js
https://d3js.org/d3.v3.min.js