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gwa.d3.5.3.1.js
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// hide context menu and SNP information if click on the outside of it
$(document).mouseup(function (e)
{
var container = $('#newContMen');
if (container.has(e.target).length === 0)
{
container.hide();
$('#tooltip').hide();
$('#zoomBar').remove();
}
});
jQuery.fn.exists = function(){return this.length>0;}
// define function to move svg-element to the front
d3.selection.prototype.moveToFront = function() {
return this.each(function(){
this.parentNode.appendChild(this);
});
};
/* User Agent (Browserkennung) auf einen bestimmten Browsertyp pr�fen */
function checkBrowserName(name){
var agent = navigator.userAgent.toLowerCase();
if (agent.indexOf(name.toLowerCase())>-1) {
return true;
}
return false;
}
function plotZoomBar(svg,options,w,h,zero,snpBeg,snpEnd,full,paddingTop,scaleW,scaleH){
if (!$('#zoomBarStat1'+options.div.replace("#","")).exists()){
svg.append("rect")
.attr("x",zero)
.attr("y",paddingTop/1.5)
.attr("id","zoomBarStat1"+options.div.replace("#",""))
.attr("height", h/30)
.attr("width", Math.round(snpBeg-zero))
.style("fill", "rgb(200,200,200)");
svg.append("rect")
.attr("x",Math.round(snpBeg))
.attr("y",paddingTop/1.5)
.attr("id","zoomBarStat2"+options.div.replace("#",""))
.attr("height",h/30)
.attr("width", Math.round(snpEnd-snpBeg))
.style("fill", "#08C");
svg.append("rect")
.attr("x",Math.round(snpEnd))
.attr("y",paddingTop/1.5)
.attr("id","zoomBarStat3"+options.div.replace("#",""))
.attr("height",h/30)
.attr("width", Math.round(full-snpEnd))
.style("fill", "rgb(200,200,200)");
svg.append("line")
.attr("x1",zero)
.attr("id","zoomLine1"+options.div.replace("#",""))
.attr("y1",scaleH(options.max_y+1))
.attr("x2",Math.round(snpBeg))
.attr("y2",paddingTop/1.5+h/30)
.style("stroke", "#08C")
.style("stroke-width",1);
svg.append("line")
.attr("x1",full)
.attr("id","zoomLine2"+options.div.replace("#",""))
.attr("y1",scaleH(options.max_y+1))
.attr("x2",Math.round(snpEnd))
.attr("y2",paddingTop/1.5+h/30)
.style("stroke", "#08C")
.style("stroke-width",1);
}
else{
$("#zoomBarStat1"+options.div.replace("#",""))
.attr("width",Math.round(snpBeg-zero));
$("#zoomBarStat2"+options.div.replace("#",""))
.attr("x",Math.round(snpBeg))
.attr("width",function(){
if ((snpEnd-snpBeg)< 5){
return 5;
}
else{
return Math.round(snpEnd-snpBeg);
}
});
}
$("#zoomBarStat3"+options.div.replace("#",""))
.attr("x",function(){
return (parseFloat($("#zoomBarStat2"+options.div.replace("#","")).attr('x'))+parseFloat($("#zoomBarStat2"+options.div.replace("#","")).attr('width')));
})
.attr("width", Math.round(full-snpEnd));
$('#zoomLine1'+options.div.replace("#",""))
.attr("x2",function(){
return $("#zoomBarStat2"+options.div.replace("#","")).attr("x")
});
$('#zoomLine2'+options.div.replace("#",""))
.attr("x2",function(){
return $("#zoomBarStat3"+options.div.replace("#","")).attr("x")
});
}
// get informations
function plotManhattanD3(attr,bp_pos_global){
//Width and height
var padding = 40;
var paddingTop = 60;
var paddingBottom = 100;
var scaleW = d3.scale.linear();
var scaleH = d3.scale.linear();
var scaleWfixed = d3.scale.linear();
var x = d3.scale.linear();
var y = d3.scale.linear();
var boxLevel = 0;
var boxNum = -1;
var options = {
task_id:undefined,
matrix: undefined,
species_id: undefined,
dataset_id: undefined,
chr: 0,
alpha: 0.05,
max_y: 10,
max_x: 10,
bonferoniThreshold: 10,
div: undefined,
divLegend: undefined,
xlabel: "x",
ylabel: "y",
legend1: "",
legend2: "",
color:0,
limited:0,
experiment_type:"GWAS"
};
//parse attr
$.extend(options,attr);
var w = d3.select(options.div).style('width').replace("px","");
var h = d3.select(options.div).style('height').replace("px","");
var divHeight = $(options.div).height();
// define scaling options
scaleW.domain([0, options.max_x]);
scaleW.range([padding, (w-padding)]);
scaleH.domain([0, options.max_y+1]);
scaleH.range([h-paddingBottom, paddingTop]);
x.domain([padding, (w-padding)]);
x.range([0, options.max_x]);
scaleWfixed.domain([0, options.max_x]);
scaleWfixed.range([padding, (w-padding)]);
var full = scaleWfixed(options.max_x);
var zero = scaleWfixed(0);
// ajax request to get tooltip-information for a single SNP
function tooltipdata(d){
var x = d[0];
var y = d[1];
var gene = "";
if (options.genome_annotation_id!=-1) {
var scriptUrl = "/gwas/results/manhattan/annotate/" + options.species_id + "/" + options.genome_annotation_id + "/" + options.chr + "/" + x + "/";
$.ajax({
url: scriptUrl,
type: 'get',
dataType: 'html',
async: false,
success: function(data) {
gene = data;
}
});
if(gene!="") {
gene = "Gene: "+gene;
}
}
y = Math.round((y*100))/100;
var mouseCoords = d3.mouse(svg[0][0].parentElement);
$('#t1').text("SNP-Pos: " + x);
$('#t2').text(options.ylabel + ": " + y);
$('#t3').text(gene);
if(options.experiment_type=="GWAS"){
$('#t4').text("Click for more information!")
$('#t4').css({"color":"#66B266","font-weight":"900"})
}
//$('#tooltip').css({"top": (d3.event.pageY-10)+"px", "left":(d3.event.pageX+10)+"px","position":"absolute","background-color":"white","padding":"2px","z-index":"10","border":"1px solid #ccc"});
$('#tooltip').css({"top": (d3.event.pageY-mouseCoords[1]-15)+"px", "left":(mouseCoords[0]+30)+"px",
"position":"absolute","background-color":"black","color":"white",
"opacity": "0.7",
"filter": "alpha(opacity=70)",
"padding":"2px","z-index":"100","border":"1px solid transparent",
"border-radius": "4px"});
/*$('#tooltip').css({"top": ($(this).offset().top-div_tip_height-10)+"px", "left":(mouseCoords[0]+10)+"px",
"position":"absolute","background-color":"black","color":"white",
"opacity": "0.7",
"filter": "alpha(opacity=70)",
"padding":"2px","z-index":"100","border":"1px solid transparent",
"border-radius": "4px"});*/
$('#tooltip').show();
// return //text
};
// define colors
var blue = 204 - (options.color) * 40;
var red = 51 + (options.color) * 40;
// get data
var data = options.matrix;
var d2 = [[0,options.bonferoniThreshold],[options.max_x,options.bonferoniThreshold]];
// draw svg
var svg = d3.select(options.div)
.append("svg")
.attr("width", w)
.attr("height", h-paddingBottom+padding);
var len = Math.pow(10,((String(Math.round(options.max_x/5)).length-1)));
var val_x = Math.round(options.max_x/5/len)*len;
var aktuell = false;
// remover highlited circles, for IE workaround
svg.on("mouseenter",function(d){
if(aktuell){
$('#tooltip').hide();
aktuell.style("fill", function(d){
if (!(d[0] == eval(bp_pos_global))){
return ("rgba("+red+",102,"+blue+",1)");
}
else{
return ("rgba("+(255-red)+","+(255-102)+","+(255-blue)+",1)");
}
})
.attr("r", 2.1).style("stroke","");
aktuell = false;
}
})
// draw graph help-lines in background
for (var i = 0; (val_x*i) < options.max_x ; i++) {
svg.append("svg:line").attr("class","helpLine")
.attr("x1", scaleW(val_x*i))
.attr("y1", scaleH(0))
.attr("x2", scaleW(val_x*i))
.attr("y2", scaleH(options.max_y+1))
.style("stroke", "#CCC")
.style("stroke-width",1);
svg.append("svg:g").attr("class","posText")
.attr("transform", "translate("+scaleW(val_x*i)+","+(h-paddingBottom/1.2)+")")
.append("text").text(val_x*i)
.attr("text-anchor", "middle");
};
var val_y = Math.round(options.max_y/3)
for (var i = 1; (i*val_y) < (options.max_y+1); i++) {
svg.append("svg:line")
.attr("x1", scaleW(0))
.attr("y1", scaleH(val_y*i))
.attr("x2", scaleW(options.max_x))
.attr("y2", scaleH(val_y*i))
.style("stroke", "#CCC")
.style("stroke-width",1);
svg.append("svg:g")
.attr("transform", "translate("+(padding/1.5)+","+scaleH(val_y*i)+")")
.append("text").text(val_y*i)
.attr("text-anchor", "middle");
};
// write text-information to axis and draw graph-elements
svg.append("svg:g")
.attr("transform", "translate("+5+","+12+")")
.append("text").text("Manhattan-plot for chromosome "+ options.chr)
.style("font-weight","bold")
svg.append("svg:g")
.attr("transform", "matrix(0, -1, 1, 0, 0, 0)").append("svg:g")
.attr("transform", "translate("+((paddingBottom-h))+","+(padding/3)+")")
.append("text").text(options.ylabel);
svg.append("svg:g")
.attr("transform", "translate("+((w-padding)/2)+","+(h-paddingBottom/1.5)+")")
.append("text").text("chromosomal position [bp]")
.attr("text-anchor", "middle");
svg.append("rect")
.attr("x", padding)
.attr("y", padding/2)
.attr("width", padding/2.5)
.attr("height", padding/3.5)
.style("fill", "rgba("+red+",102,"+blue+",1)");
svg.append("svg:g")
.attr("transform", "translate("+(padding+25)+","+(padding/1.3)+")")
.append("text").text(options.legend1);
svg.append("rect")
.attr("x", padding*5.5)
.attr("y", padding/2)
.attr("width", padding/2.5)
.attr("height", padding/3.5)
.style("fill", "rgb(0,100,0)");
svg.append("svg:line")
.attr("x1", scaleW(0))
.attr("y1", scaleH(options.max_y+1))
.attr("x2", scaleW(options.max_x))
.attr("y2", scaleH(options.max_y+1))
.style("stroke", "#CCC")
.style("stroke-width",1.5 );
svg.append("svg:line")
.attr("x1", scaleW(options.max_x))
.attr("y1", scaleH(0))
.attr("x2", scaleW(options.max_x))
.attr("y2", scaleH(options.max_y+1))
.style("stroke", "#CCC")
.style("stroke-width",1.5 );
svg.append("svg:line")
.attr("x1", scaleW(0))
.attr("y1", scaleH(0))
.attr("x2", scaleW(0))
.attr("y2", scaleH(options.max_y+1))
.style("stroke", "#000000")
.style("stroke-width",1);
svg.append("svg:line")
.attr("x1", scaleW(0))
.attr("y1", scaleH(0))
.attr("x2", scaleW(options.max_x))
.attr("y2", scaleH(0))
.style("stroke", "#000000")
.style("stroke-width",1);
svg.append("svg:g")
.attr("transform", "translate("+(padding*5.5+25)+","+(padding/1.3)+")")
.append("text").text(options.legend2);
svg.append("svg:line")
.attr("x1", scaleW(d2[0][0]))
.attr("y1", scaleH(d2[0][1]))
.attr("x2", scaleW(d2[1][0]))
.attr("y2", scaleH(d2[1][1]))
.style("stroke", "rgb(0,100,0)")
.style("stroke-width",1.5 );
// draw datapoints
if(checkBrowserName('MSIE')){
var aktuell = false;
svg.selectAll("circle")
.data(data)
.enter()
.append("circle")
.attr("cx", function(d) {
return scaleW(d[0]);
})
.attr("cy", function(d) {
return scaleH(d[1]);
})
.attr("r", 2.1)
.style("fill", function(d){
if (!(d[0] == eval(bp_pos_global))){
return ("rgba("+red+",102,"+blue+",1)");
}
else{
return ("rgba("+(255-red)+","+(255-102)+","+(255-blue)+",1)");
}
})
.on("mouseenter",function(d){
if (!aktuell){
d3.select(this).style("stroke", "rgba("+(255-red)+","+(255-102)+","+(255-blue)+",0.65)").style("stroke-width",10 );
d3.select(this).style("fill", "rgba("+(255-red)+","+(255-102)+","+(255-blue)+",1)").moveToFront();
d3.select(this).attr("z-index","1000");
tooltipdata(d);
aktuell = d3.select(this);
}
});
}
else {
svg.selectAll("circle")
.data(data)
.enter()
.append("circle")
.attr("cx", function(d) {
return scaleW(d[0]);
})
.attr("cy", function(d) {
return scaleH(d[1]);
})
.attr("r", 2.1)
.style("fill", function(d){
if (!(d[0] == eval(bp_pos_global))){
return ("rgba("+red+",102,"+blue+",0.65)");
}
else{
return ("rgba("+(255-red)+","+(255-102)+","+(255-blue)+",0.65)");
}
})
.on("mouseover",function(d){
d3.select(this).style("stroke", "rgba("+(255-red)+","+(255-102)+","+(255-blue)+",0.65)").style("stroke-width",10 );
d3.select(this).style("fill", "rgba("+(255-red)+","+(255-102)+","+(255-blue)+",0.65)").moveToFront();
d3.select(this).attr("z-index","1000");
tooltipdata(d);
})
.on("mouseout", function(){
$('#tooltip').hide();
d3.select(this).style("fill", function(d){
if (!(d[0] == eval(bp_pos_global))){
return ("rgba("+red+",102,"+blue+",0.65)");
}
else{
return ("rgba("+(255-red)+","+(255-102)+","+(255-blue)+",0.65)");
}
})
.attr("r", 2.1).style("stroke","");
});
}
//////////////////////////////////////////////// detailed SNP-View on click ======================================================================>>>>>
if(options.experiment_type=="GWAS") {
svg.selectAll("circle").data(data).on("click", function(d){
window.location.href = '/gwas/results/snp/detailed/'+options.task_id+'/'+options.chr+'/'+d[0]+'/';
});
}
//<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< end detailed SNP-View on db-click ============================================================/////////////////////////
var xBeg,yBeg,xNow,yNow,xEnd,yEnd;
var isWebkit = (window.URL != null);
if(!bp_pos_global){
svg.on("mousedown",function(){
if(isWebkit){
var mouseCoords = d3.mouse(svg[0][0].parentElement);
xBeg = mouseCoords[0];
} else {
xBeg = d3.event.pageX;
}
svg.append("rect")
.attr("id","zoomBar")
.attr("x", xBeg-0.02)
.attr("y", scaleH(options.max_y+1))
.attr("width", 0)
.attr("height", scaleH(0)-scaleH(options.max_y+1))
.style("fill", "rgba(184,184,184,0.5)");
d3.event.preventDefault();
svg.on("mousemove",function(){
if(isWebkit) {
var mouseCoords = d3.mouse(svg[0][0].parentElement);
xNow = mouseCoords[0];
} else {
xNow= d3.event.pageX;
}
if (xNow > xBeg){
$('#zoomBar').attr("width",(xNow-xBeg));
}
if (xNow < xBeg){
$('#zoomBar').attr("x", (xNow)).attr("width",Math.abs(xBeg-xNow));
d3.event.preventDefault();
}
});
svg.on("mouseup",function(d){
xWidth = $(this).width();
if(isWebkit) {
var mouseCoords = d3.mouse(svg[0][0].parentElement);
xEnd = mouseCoords[0];
} else {
xEnd = d3.event.pageX;
}
$('#zoomBar').remove();
zoom();
});
});
svg.on("contextmenu",function(){
$(options.div).height(255);
$(this).remove();
plotManhattanD3(attr);
$('#zoomBarStat1').remove();
$('#zoomBarStat2').remove();
$('#zoomBarStat3').remove();
$('.geneBox').remove();
$('#TtooltipGene').hide();
boxLevel = 0;
boxNum = -1;
d3.event.preventDefault();
return false;
});
}
else{
svg.on("contextmenu",function(){
$(options.div).height(255);
$(this).remove();
d3.event.preventDefault();
$('#zoomBarStat1').remove();
$('#zoomBarStat2').remove();
$('#zoomBarStat3').remove();
$('.geneBox').remove();
$('#TtooltipGene').hide();
boxLevel = 0;
boxNum = -1;
plotManhattanD3(attr,bp_pos_global);
return false;
});
}
$('#loader').remove();
function zoom(){
var beg = Math.round(x(xBeg));
var end = Math.round(x(xEnd));
var tmp;
if (beg > end){
tmp = beg;
beg = end;
end = tmp;
}
var snpBeg = scaleWfixed(beg);
var snpEnd = scaleWfixed(end);
if ((end-beg) <= 2){
return false
}
x.range([beg, end]);
scaleW.domain([beg,end]);
/////////////////////////////////////////////////////////////// geneView ===============================================================>>
// only calculate and draw genes, if checkbox is checked
if ($("#showGenes").attr('checked') || (bp_pos_global)){
var beg_pos = beg-10000;
if(beg_pos<0) beg_pos=0;
var annos = $.getJSON("/gwas/results/manhattan/annotate/plot/"+options.species_id+"/"+options.genome_annotation_id+"/"+options.chr+"/"+beg_pos+"/"+(end+10000)+"/",function(data){
// if (data.anno.length >=100) {return } //IMPORTANT!!! sets max. number of genes displayed
var tooltipGene = new Array();
var geneLevelClosed = new Array();
var geneLevel = 0;
var yGene = new Array();
geneLevelClosed[0] = scaleW(data.anno[0][2]);
yGene[0] = 0;
//calculate level where gene is displayed
for(i=1; i < (data.anno.length) ; i++){
for(l=0; l <= geneLevel ; l++){
if((geneLevelClosed[l]) <= scaleW(data.anno[i][1])){
yGene[i] = l;
if (Math.abs(scaleW(data.anno[i][1])-scaleW(data.anno[i][1])) < 10){
geneLevelClosed[l] = scaleW(data.anno[i][2])+10;
}
else{
geneLevelClosed[l] = scaleW(data.anno[i][2]);
}
break;
}
else if(l == geneLevel){
geneLevel += 1;
geneLevelClosed[geneLevel] = scaleW(0);
}
}
}
// display genes
for(i=0; i < data.anno.length ; i++){
tooltipGene[data.anno[i][0]] = new Array(data.anno[i][1], data.anno[i][2], data.anno[i][3])
drawArrow(data,i,tooltipGene,yGene,beg,end);
}
//resize div/svg to updated size, influenced by genes
$(options.div).height(divHeight+geneLevel*10);
svg.attr('height',$(options.div).height());
});
}
//========================================================================>> geneView /////////////////////////////////////////////////////////
else {
// if no genes displayed, restore original div/svg size
$(options.div).height(divHeight);
svg.attr('height',$(options.div).height());
}
var t = svg.transition()
.duration(750);
t.selectAll("circle")
.attr("cx", function(d) {
if((d[0] > beg) && (d[0] < end)){
return scaleW(d[0]);
}
else {
$(this).remove();
}
});
svg.selectAll(".helpLine").remove();
svg.selectAll(".posText").remove();
svg.selectAll(".gene").remove();
svg.selectAll(".geneAnno").remove();
svg.selectAll(".geneBox").remove();
boxLevel = 0;
boxNum = -1;
var len = Math.pow(10,((String(Math.round((end-beg)/5)).length-1)));
if (len == 0){
len =1;
}
var val_x = Math.round((end-beg)/5/len)*len;
// draw graph help-lines in background
for (var i = 0; (val_x*i) < options.max_x ; i++) {
if (((val_x*i) >= beg) && ((val_x*i) <= end)){
svg.append("svg:line").attr("class","helpLine")
.attr("x1", scaleW(val_x*i))
.attr("y1", scaleH(0))
.attr("x2", scaleW(val_x*i))
.attr("y2", scaleH(options.max_y+1))
.style("stroke", "#CCC")
.style("stroke-width",1);
svg.append("svg:g").attr("class","posText")
.attr("transform", "translate("+scaleW(val_x*i)+","+(h-paddingBottom/1.2)+")")
.append("text").text(val_x*i)
.attr("text-anchor", "middle");
}
};
plotZoomBar(svg,options,w,h,zero,snpBeg,snpEnd,full,paddingTop,scaleW,scaleH);
if (!bp_pos_global){
d3.event.stopPropagation();
}
}
///////////////////////////////////////////////////////draw Arrow ===========================================================>
// uncomment for production
var lineData;
//var startArrow;
//var endArrow;
var hArr = 4;
//var yArr;
//var orientationArr;
//var tooltipGene;
function drawArrow(data,i,tooltipGene,yGene,beg,end){
if ((data.anno[i][2] < beg) | (data.anno[i][1] > end)) return;
// remove for production
var ArrName = data.anno[i][0];
var ArrStart = data.anno[i][1];
var ArrEnd = data.anno[i][2];
// remove "var" for production
var startArrow = scaleW(data.anno[i][1]);
var endArrow = scaleW(data.anno[i][2]);
var orientationArr = data.anno[i][3];
var tooltipGene = tooltipGene
var yArr = (h-paddingBottom+yGene[i]*(10)+40);
var lenArr = Math.abs(startArrow - endArrow);
if (lenArr < 10) lenArr = 10;
lineData = function(){
// special case, arrow begins too left, shorten arrow & print red mark
if (parseInt(data.anno[i][1]) < beg){
startArrow = scaleW(beg);
lenArr = Math.abs(startArrow - endArrow);
svg.append("svg:rect")
.attr("class","geneAnno")
.attr("x",(startArrow))
.attr("y",(yArr-0.5*hArr))
.attr("width",1)
.attr("height",(2*hArr))
.attr("fill","red")
.attr("stroke","red")
.attr("stroke-width",2);
}
// special case, arrow ends too right, shorten arrow & print red mark
if (parseInt(data.anno[i][2]) > end){
endArrow = scaleW(end);
lenArr = Math.abs(startArrow - endArrow);
svg.append("svg:rect")
.attr("class","geneAnno")
.attr("x",(endArrow-1))
.attr("y",(yArr-0.5*hArr))
.attr("width",1)
.attr("height",(2*hArr))
.attr("fill","red")
.attr("stroke","red")
.attr("stroke-width",2);
}
// coordinates for arrow
if(orientationArr == "+"){
// path for arrow to right side
var l = [{"x": (startArrow), "y": (yArr) },
{"x": (startArrow+lenArr-(1.5*hArr)), "y": (yArr)},
{"x": (startArrow+lenArr-(1.5*hArr)), "y": (yArr-(0.5*hArr))},
{"x": (startArrow+lenArr), "y": (yArr+(0.5*hArr))},
{"x": (startArrow+lenArr-(1.5*hArr)), "y": (yArr+(1.5*hArr))},
{"x": (startArrow+lenArr-(1.5*hArr)), "y": (yArr+hArr)},
{"x": (startArrow), "y": (yArr+hArr)},
{"x": (startArrow), "y": (yArr)}]
}
else {
// path for arrow to left side
var l = [
{"x": (startArrow), "y": (yArr+(0.5*hArr))},
{"x": (startArrow+(1.5*hArr)), "y": (yArr-(0.5*hArr))},
{"x": (startArrow+(1.5*hArr)), "y": (yArr)},
{"x": (startArrow+lenArr), "y": (yArr) },
{"x": (startArrow+lenArr), "y": (yArr+hArr)},
{"x": (startArrow+(1.5*hArr)), "y": (yArr+hArr)},
{"x": (startArrow+(1.5*hArr)), "y": (yArr+(1.5*hArr))},
{"x": (startArrow), "y": (yArr+(0.5*hArr))},
]
}
return l;
};
// returns arrows as path
var lineFunction = d3.svg.line()
.x(function(d) { return d.x; })
.y(function(d) { return d.y; });
// draw arrow, use path constructed from coordinates
var lineGraph = svg.append("path")
.attr("d", lineFunction(lineData()))
.attr("stroke", "#7C7C7C")
.attr("class","geneAnno")
.attr("stroke-width", 1)
.attr("fill", function(){
if (orientationArr == "+") return "#AEC6CF";//"#62D6F6";
return "#FFB347"})//"#D7F63C"})
.attr("id",data.anno[i][0])
// show tooltip on hover
.on("mouseover", function(){
var mouseCoords = d3.mouse(svg[0][0].parentElement);
var div_tip_height = parseFloat($('#Ttooltip').height());
$('#tt1').text("Name: "+this.id);
$('#tt2').text("Start Position: "+tooltipGene[this.id][0]);
$('#tt3').text("End Position: "+tooltipGene[this.id][1]);
$('#tt4').text("Strand: "+tooltipGene[this.id][2]);
//$('#Ttooltip').css({"top": (d3.event.pageY-10)+"px", "left":(d3.event.pageX+10)+"px","position":"absolute","background-color":"white","padding":"2px","z-index":"10","border":"1px solid #ccc"});
$('#Ttooltip').css({"top": ($(this).offset().top-div_tip_height-60)+"px", "left":(mouseCoords[0]+30)+"px",
"position":"absolute","background-color":"black","color":"white",
"opacity": "0.7",
"filter": "alpha(opacity=70)",
"padding":"2px","z-index":"100","border":"1px solid transparent",
"border-radius": "4px"});
$('#Ttooltip').show();
})
// hide tooltip
.on("mouseout", function(){
$('#Ttooltip').hide();
})
// show fixed tooltip on click
/*.on("click", function(d) {
var mouseCoords = d3.mouse(svg[0][0].parentElement);
$('#ttt1').text("Name: "+this.id);
$('#ttt2').text("Start Position: "+tooltipGene[this.id][0]);
$('#ttt3').text("End Position: "+tooltipGene[this.id][1]);
$('#ttt4').text("Strand: "+tooltipGene[this.id][2]);
//$('#TtooltipGene').css({"top": (d3.event.pageY+3)+"px", "left":(d3.event.pageX+3)+"px","position":"absolute","background-color":"white","padding":"2px","z-index":"5","border":"1px solid #ccc"});
$('#TtooltipGene').css({"top": (d3.event.pageY-mouseCoords[1]-3)+"px", "left":(mouseCoords[0]+3)+"px",
"position":"absolute","background-color":"black","color":"white",
"opacity": "0.7",
"filter": "alpha(opacity=70)",
"padding":"2px","z-index":"100","border":"1px solid transparent",
"border-radius": "4px"});
$('#TtooltipGene').show()})
*/
// draw gene-information on doublecklick
.on("dblclick", function(d) {
drawGeneInfo(Math.max.apply(null,yGene),yGene[i],yArr,hArr,data.anno[i][0],data.anno[i][1],data.anno[i][2],data.anno[i][3],beg,end,startArrow);
d3.event.preventDefault();
});
}
// hide fixed gene-tooltip
/*
$('#TtooltipGene').on("click", function() {
$('#TtooltipGene').hide();
});
*/
//====================================================>draw Arrow \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
///////////////////////////////////////////////////////draw custom gene info ===========================================================>
function drawGeneInfo(yMax,yGene,yArr,hArr,geneName,geneBeg,geneEnd,geneOrientation,beg,end,startArrow){
var boxSpaceBeg = scaleW(beg);
var boxSpaceEnd = scaleW(end);
var boxHeight = 70;
var boxWidth = 170;
var textSizeGene = 3;
var yPaddingText = 15;
var xPaddingText = 4;
var paddingText = 15;
var boxSpaceUsed = (scaleW(beg)+(boxWidth*boxNum));
var yBox = (h-paddingBottom+(yMax*10)+50+boxLevel*boxHeight);
if((boxSpaceUsed+2*boxWidth) > boxSpaceEnd){
boxLevel += 1;
boxNum = 0;
}
else{
boxNum += 1;
}
boxSpaceUsed = (scaleW(beg)+(boxWidth*boxNum));
yBox = (h-paddingBottom+(yMax*10)+50+boxLevel*boxHeight);
$(options.div).height(divHeight+yMax*10+boxHeight*boxLevel+20);
svg.attr('height',$(options.div).height());
svg.append("svg:rect")
.attr("x",boxSpaceUsed)
.attr("y",yBox)
.attr("width",boxWidth-4)
.attr("height",boxHeight-4)
.attr("stroke","black")
.attr("stroke-width",1)
.attr("fill","white")
.attr("class","geneBox")
.attr("id",geneName+"box");
svg.append("svg:g")
.attr("transform", "translate("+(boxSpaceUsed+xPaddingText)+","+(yBox+yPaddingText)+")")
.append("text").text("Name: "+geneName)
.attr("class","geneBox")
.attr("size",textSizeGene);
svg.append("svg:g")
.attr("transform", "translate("+(boxSpaceUsed+xPaddingText)+","+(yBox+yPaddingText+paddingText)+")")
.append("text").text("Start Position: "+geneBeg)
.attr("class","geneBox")
.attr("size",textSizeGene);
svg.append("svg:g")
.attr("transform", "translate("+(boxSpaceUsed+xPaddingText)+","+(yBox+yPaddingText+(+paddingText*2))+")")
.append("text").text("End Position: "+geneEnd)
.attr("class","geneBox")
.attr("size",textSizeGene);
svg.append("svg:g")
.attr("transform", "translate("+(boxSpaceUsed+xPaddingText)+","+(yBox+yPaddingText+(paddingText*3))+")")
.append("text").text("Strand: "+geneOrientation)
.attr("class","geneBox")
.attr("size",textSizeGene);
lineDataBox = function(){
var l = [
{"x": (boxSpaceUsed), "y": (yBox)},
{"x": (startArrow+2), "y": (yArr+0.5*hArr)},]
return l;
}
var lineFunctionBox = d3.svg.line()
.x(function(d) { return d.x; })
.y(function(d) { return d.y; });
var lineGraph = svg.append("path")
.attr("d", lineFunctionBox(lineDataBox()))
.attr("stroke", "black")
.attr("class","geneBox")
.style("stroke-opacity", 0.6)
.attr("stroke-width", 1);
$('#TtooltipGene').hide();
}
//====================================================>draw custom gene info \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
if(bp_pos_global){
zoom(bp_pos_global);
}
}
function plotHistogram(attr){
var options = {
matrix: undefined,
max_y: 15,
max_x: 7,
min_x: 0,
div: undefined,
divLegend: undefined,
xlabel: "x",
ylabel: "y",
legend1: "",
legend2: "",
barWidth:0.3,
toolbox_label:"Phenotype range",
lastBin:0.0,
ranges:undefined
};
var privateBarColor = "#f0ad4e";
var private_hover = "#9E5B00";
var private_stroke = "#C78425"
var publicBarColor = "#4cae4c";
var public_hover = "#238523";
var public_stroke = "#005C00"
//parse attr
$.extend(options,attr);
var data = options.matrix;
var padding = 35;
var w = d3.select(options.div).style('width').replace("px","");
var h = d3.select(options.div).style('height').replace("px","");
var scaleW = d3.scale.linear();
var scaleH = d3.scale.linear();
if (options.color==1) {
barColor = privateBarColor;
hover = private_hover;
stroke = private_stroke;
} else {
barColor = publicBarColor;
hover = public_hover;
stroke = public_stroke;
}
//var blue = 204 - (options.color) * 40;
//var red = 51 + (options.color) * 40;
//var barColor = "rgb(" + red + ",102," + blue + ")";
// define scaling options
scaleW.domain([options.min_x, options.max_x]);
scaleW.range([padding, w-padding]);
scaleH.domain([0, options.max_y+1]);
scaleH.range([h-padding, padding]);
var svg = d3.select(options.div)
.append("svg")
.attr("width", w)
.attr("height", h);
var aktuell = false;
/*
// remover highlited circles, for IE workaround
svg.on("mouseenter",function(d){
if(aktuell){
$('#tooltip').hide();
// d3.select(".bars").attr("fill", barColor);
svg.selectAll(".bars").attr("fill", barColor);
aktuell = false;
}
})