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biocircos-1.1.1.js
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biocircos-1.1.1.js
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/**
* BioCircos.js is an open source interactive Javascript library which
* provides an easy way to interactive display biological data on the web.
* It implements a raster-based SVG visualization using the open source
* Javascript framework jquery.js. BioCircos.js is multiplatform and works
* in all major internet browsers (Internet Explorer, Mozilla Firefox,
* Google Chrome, Safari, Opera). Its speed is determined by the client's
* hardware and internet browser. For smoothest user experience, we recommend
* Google Chrome.
*
* Source code, tutorial, documentation, and example data are freely available
* from BioCircos.js website "http://bioinfo.ibp.ac.cn/biocircos/".
*
* @author <a href="[email protected]">Ya Cui</a>, <a href="[email protected]">Xiaowei Chen</a>
* @version 1.1.1
*
* @example
* var BioCircosGenome = [
* ["chr1" , 249250621],
* ["chr2" , 243199373]
* ];
* BioCircos01 = new BioCircos(BioCircosGenome,{
* target : "biocircos",
* svgWidth : 900,
* svgHeight : 600
* });
* BioCircos01.draw_genome(BioCircos01.genomeLength);
*
**/
var BioCircos;
(function($){
BioCircos = function(){
var self = this;
if(arguments.length >= 2){
self.argumentsBiocircosSettings=arguments[arguments.length-1];
self.argumentsBiocircosGenome=arguments[arguments.length-2];
self.CNV = new Array();
self.CNVConfig = new Array();
for (var n=0; n< arguments.length; n++){
var reg=/^CNV/;
if(reg.test(arguments[n][0])){
self.CNVConfig.push(arguments[n][1]);
self.CNV.push(arguments[n][2]);
}
}
self.HEATMAP = new Array();
self.HEATMAPConfig = new Array();
for (var n=0; n< arguments.length; n++){
var reg=/^HEATMAP/;
if(reg.test(arguments[n][0])){
self.HEATMAPConfig.push(arguments[n][1]);
self.HEATMAP.push(arguments[n][2]);
}
}
self.SNP = new Array();
self.SNPConfig = new Array();
for (var n=0; n< arguments.length; n++){
var reg=/^SNP/;
if(reg.test(arguments[n][0])){
self.SNPConfig.push(arguments[n][1]);
self.SNP.push(arguments[n][2]);
}
}
self.LINK = new Array();
self.LINKConfig = new Array();
for (var n=0; n< arguments.length; n++){
var reg=/^LINK/;
if(reg.test(arguments[n][0])){
self.LINKConfig.push(arguments[n][1]);
self.LINK.push(arguments[n][2]);
}
}
self.HISTOGRAM = new Array();
self.HISTOGRAMConfig = new Array();
for (var n=0; n< arguments.length; n++){
var reg=/^HISTOGRAM/;
if(reg.test(arguments[n][0])){
self.HISTOGRAMConfig.push(arguments[n][1]);
self.HISTOGRAM.push(arguments[n][2]);
}
}
self.LINE = new Array();
self.LINEConfig = new Array();
for (var n=0; n< arguments.length; n++){
var reg=/^LINE/;
if(reg.test(arguments[n][0])){
self.LINEConfig.push(arguments[n][1]);
self.LINE.push(arguments[n][2]);
}
}
self.SCATTER = new Array();
self.SCATTERConfig = new Array();
for (var n=0; n< arguments.length; n++){
var reg=/^SCATTER/;
if(reg.test(arguments[n][0])){
self.SCATTERConfig.push(arguments[n][1]);
self.SCATTER.push(arguments[n][2]);
}
}
self.BACKGROUND = new Array();
self.BACKGROUNDConfig = new Array();
for (var n=0; n< arguments.length; n++){
var reg=/^BACKGROUND/;
if(reg.test(arguments[n][0])){
self.BACKGROUNDConfig.push(arguments[n][1]);
self.BACKGROUND.push(arguments[n][2]);
}
}
self.TEXT = new Array();
self.TEXTConfig = new Array();
for (var n=0; n< arguments.length; n++){
var reg=/^TEXT/;
if(reg.test(arguments[n][0])){
self.TEXTConfig.push(arguments[n][1]);
self.TEXT.push(arguments[n][2]);
}
}
self.ARC = new Array();
self.ARCConfig = new Array();
for (var n=0; n< arguments.length; n++){
var reg=/^ARC/;
if(reg.test(arguments[n][0])){
self.ARCConfig.push(arguments[n][1]);
self.ARC.push(arguments[n][2]);
}
}
}else{
document.getElementById(self.settings.target).innerHTML='Arguments Error: at least two arguments must supplied.<br>example: new BioCircos([FUSION01,CNV01,SNP01,]BioCircosGenome,{target : "biocircos",zoom : true})';
}
self.settings = {
"target" : "biocircos",
"svgWidth" : 900,
"svgHeight" : 600,
"chrPad" : 0.04,
"innerRadius" : 246,
"outerRadius" : 270,
"zoom" : false,
"genomeFillColor" : ["rgb(153,102,0)", "rgb(102,102,0)", "rgb(153,153,30)", "rgb(204,0,0)","rgb(255,0,0)", "rgb(255,0,204)", "rgb(255,204,204)", "rgb(255,153,0)", "rgb(255,204,0)", "rgb(255,255,0)", "rgb(204,255,0)", "rgb(0,255,0)","rgb(53,128,0)", "rgb(0,0,204)", "rgb(102,153,255)", "rgb(153,204,255)", "rgb(0,255,255)", "rgb(204,255,255)", "rgb(153,0,204)", "rgb(204,51,255)","rgb(204,153,255)", "rgb(102,102,102)", "rgb(153,153,153)", "rgb(204,204,204)"],
"CNVMouseEvent" : true,
"CNVMouseClickDisplay" : false,
"CNVMouseClickColor" : "red",
"CNVMouseClickArcOpacity" : 1.0,
"CNVMouseClickArcStrokeColor" : "#F26223",
"CNVMouseClickArcStrokeWidth" : 0,
"CNVMouseClickTextFromData" : "fourth", //first,second,third,fourth column
"CNVMouseClickTextOpacity" : 1,
"CNVMouseClickTextColor" : "red",
"CNVMouseClickTextSize" : 8,
"CNVMouseClickTextPostionX" : 0,
"CNVMouseClickTextPostionY" : 0,
"CNVMouseClickTextDrag" : true,
"CNVMouseDownDisplay" : false,
"CNVMouseDownColor" : "green",
"CNVMouseDownArcOpacity" : 1.0,
"CNVMouseDownArcStrokeColor" : "#F26223",
"CNVMouseDownArcStrokeWidth" : 0,
"CNVMouseEnterDisplay" : false,
"CNVMouseEnterColor" : "yellow",
"CNVMouseEnterArcOpacity" : 1.0,
"CNVMouseEnterArcStrokeColor" : "#F26223",
"CNVMouseEnterArcStrokeWidth" : 0,
"CNVMouseLeaveDisplay" : false,
"CNVMouseLeaveColor" : "pink",
"CNVMouseLeaveArcOpacity" : 1.0,
"CNVMouseLeaveArcStrokeColor" : "#F26223",
"CNVMouseLeaveArcStrokeWidth" : 0,
"CNVMouseMoveDisplay" : false,
"CNVMouseMoveColor" : "red",
"CNVMouseMoveArcOpacity" : 1.0,
"CNVMouseMoveArcStrokeColor" : "#F26223",
"CNVMouseMoveArcStrokeWidth" : 0,
"CNVMouseOutDisplay" : false,
"CNVMouseOutAnimationTime" : 500,
"CNVMouseOutColor" : "red",
"CNVMouseOutArcOpacity" : 1.0,
"CNVMouseOutArcStrokeColor" : "red",
"CNVMouseOutArcStrokeWidth" : 0,
"CNVMouseUpDisplay" : false,
"CNVMouseUpColor" : "grey",
"CNVMouseUpArcOpacity" : 1.0,
"CNVMouseUpArcStrokeColor" : "#F26223",
"CNVMouseUpArcStrokeWidth" : 0,
"CNVMouseOverDisplay" : false,
"CNVMouseOverColor" : "red",
"CNVMouseOverArcOpacity" : 1.0,
"CNVMouseOverArcStrokeColor" : "#F26223",
"CNVMouseOverArcStrokeWidth" : 3,
"CNVMouseOverTooltipsHtml01" : "chr : ",
"CNVMouseOverTooltipsHtml02" : "<br>start : ",
"CNVMouseOverTooltipsHtml03" : "<br>end : ",
"CNVMouseOverTooltipsHtml04" : "<br>value : ",
"CNVMouseOverTooltipsHtml05" : "",
"CNVMouseOverTooltipsPosition" : "absolute",
"CNVMouseOverTooltipsBackgroundColor" : "white",
"CNVMouseOverTooltipsBorderStyle" : "solid",
"CNVMouseOverTooltipsBorderWidth" : 0,
"CNVMouseOverTooltipsPadding" : "3px",
"CNVMouseOverTooltipsBorderRadius" : "3px",
"CNVMouseOverTooltipsOpacity" : 0.8,
"HEATMAPMouseEvent" : true,
"HEATMAPMouseClickDisplay" : false,
"HEATMAPMouseClickColor" : "green", //"none","red"
"HEATMAPMouseClickOpacity" : 1.0, //"none",1.0
"HEATMAPMouseClickStrokeColor" : "none", //"none","#F26223"
"HEATMAPMouseClickStrokeWidth" : "none", //"none",3
"HEATMAPMouseDownDisplay" : false,
"HEATMAPMouseDownColor" : "green", //"none","red"
"HEATMAPMouseDownOpacity" : 1.0, //"none",1.0
"HEATMAPMouseDownStrokeColor" : "none", //"none","#F26223"
"HEATMAPMouseDownStrokeWidth" : "none", //"none",3
"HEATMAPMouseEnterDisplay" : false,
"HEATMAPMouseEnterColor" : "green", //"none","red"
"HEATMAPMouseEnterOpacity" : 1.0, //"none",1.0
"HEATMAPMouseEnterStrokeColor" : "none", //"none","#F26223"
"HEATMAPMouseEnterStrokeWidth" : "none", //"none",3
"HEATMAPMouseLeaveDisplay" : false,
"HEATMAPMouseLeaveColor" : "green", //"none","red"
"HEATMAPMouseLeaveOpacity" : 1.0, //"none",1.0
"HEATMAPMouseLeaveStrokeColor" : "none", //"none","#F26223"
"HEATMAPMouseLeaveStrokeWidth" : "none", //"none",3
"HEATMAPMouseMoveDisplay" : false,
"HEATMAPMouseMoveColor" : "green", //"none","red"
"HEATMAPMouseMoveOpacity" : 1.0, //"none",1.0
"HEATMAPMouseMoveStrokeColor" : "none", //"none","#F26223"
"HEATMAPMouseMoveStrokeWidth" : "none", //"none",3
"HEATMAPMouseOutDisplay" : false,
"HEATMAPMouseOutAnimationTime" : 500,
"HEATMAPMouseOutColor" : "green", //"none","red"
"HEATMAPMouseOutOpacity" : 1.0, //"none",1.0
"HEATMAPMouseOutStrokeColor" : "none", //"none","#F26223"
"HEATMAPMouseOutStrokeWidth" : "none", //"none",3
"HEATMAPMouseUpDisplay" : false,
"HEATMAPMouseUpColor" : "green", //"none","red"
"HEATMAPMouseUpOpacity" : 1.0, //"none",1.0
"HEATMAPMouseUpStrokeColor" : "none", //"none","#F26223"
"HEATMAPMouseUpStrokeWidth" : "none", //"none",3
"HEATMAPMouseOverDisplay" : false,
"HEATMAPMouseOverColor" : "none", //"none","red"
"HEATMAPMouseOverOpacity" : 1.0, //"none",1.0
"HEATMAPMouseOverStrokeColor" : "none", //"none","#F26223"
"HEATMAPMouseOverStrokeWidth" : "none", //"none",3
"HEATMAPMouseOverTooltipsHtml01" : "chr : ",
"HEATMAPMouseOverTooltipsHtml02" : "<br>position: ",
"HEATMAPMouseOverTooltipsHtml03" : "-",
"HEATMAPMouseOverTooltipsHtml04" : "<br>name : ",
"HEATMAPMouseOverTooltipsHtml05" : "<br>value : ",
"HEATMAPMouseOverTooltipsHtml06" : "",
"HEATMAPMouseOverTooltipsPosition" : "absolute",
"HEATMAPMouseOverTooltipsBackgroundColor" : "white",
"HEATMAPMouseOverTooltipsBorderStyle" : "solid",
"HEATMAPMouseOverTooltipsBorderWidth" : 0,
"HEATMAPMouseOverTooltipsPadding" : "3px",
"HEATMAPMouseOverTooltipsBorderRadius" : "3px",
"HEATMAPMouseOverTooltipsOpacity" : 0.8,
"SNPMouseEvent" : true,
"SNPMouseClickDisplay" : false,
"SNPMouseClickColor" : "red",
"SNPMouseClickCircleSize" : 4,
"SNPMouseClickCircleOpacity" : 1.0,
"SNPMouseClickCircleStrokeColor" : "#F26223",
"SNPMouseClickCircleStrokeWidth" : 0,
"SNPMouseClickTextFromData" : "fourth", //first,second,third,fourth column
"SNPMouseClickTextOpacity" : 1.0,
"SNPMouseClickTextColor" : "red",
"SNPMouseClickTextSize" : 8,
"SNPMouseClickTextPostionX" : 1.0,
"SNPMouseClickTextPostionY" : 10.0,
"SNPMouseClickTextDrag" : true,
"SNPMouseDownDisplay" : false,
"SNPMouseDownColor" : "green",
"SNPMouseDownCircleSize" : 4,
"SNPMouseDownCircleOpacity" : 1.0,
"SNPMouseDownCircleStrokeColor" : "#F26223",
"SNPMouseDownCircleStrokeWidth" : 0,
"SNPMouseEnterDisplay" : false,
"SNPMouseEnterColor" : "yellow",
"SNPMouseEnterCircleSize" : 4,
"SNPMouseEnterCircleOpacity" : 1.0,
"SNPMouseEnterCircleStrokeColor" : "#F26223",
"SNPMouseEnterCircleStrokeWidth" : 0,
"SNPMouseLeaveDisplay" : false,
"SNPMouseLeaveColor" : "pink",
"SNPMouseLeaveCircleSize" : 4,
"SNPMouseLeaveCircleOpacity" : 1.0,
"SNPMouseLeaveCircleStrokeColor" : "#F26223",
"SNPMouseLeaveCircleStrokeWidth" : 0,
"SNPMouseMoveDisplay" : false,
"SNPMouseMoveColor" : "red",
"SNPMouseMoveCircleSize" : 2,
"SNPMouseMoveCircleOpacity" : 1.0,
"SNPMouseMoveCircleStrokeColor" : "#F26223",
"SNPMouseMoveCircleStrokeWidth" : 0,
"SNPMouseOutDisplay" : false,
"SNPMouseOutAnimationTime" : 500,
"SNPMouseOutColor" : "red",
"SNPMouseOutCircleSize" : 2,
"SNPMouseOutCircleOpacity" : 1.0,
"SNPMouseOutCircleStrokeColor" : "red",
"SNPMouseOutCircleStrokeWidth" : 0,
"SNPMouseUpDisplay" : false,
"SNPMouseUpColor" : "grey",
"SNPMouseUpCircleSize" : 4,
"SNPMouseUpCircleOpacity" : 1.0,
"SNPMouseUpCircleStrokeColor" : "#F26223",
"SNPMouseUpCircleStrokeWidth" : 0,
"SNPMouseOverDisplay" : false,
"SNPMouseOverColor" : "red",
"SNPMouseOverCircleSize" : 2,
"SNPMouseOverCircleOpacity" : 1.0,
"SNPMouseOverCircleStrokeColor" : "#F26223",
"SNPMouseOverCircleStrokeWidth" : 3,
"SNPMouseOverTooltipsHtml01" : "chr : ",
"SNPMouseOverTooltipsHtml02" : "<br>position : ",
"SNPMouseOverTooltipsHtml03" : "<br>value : ",
"SNPMouseOverTooltipsHtml04" : "<br>des : ",
"SNPMouseOverTooltipsHtml05" : "",
"SNPMouseOverTooltipsPosition" : "absolute",
"SNPMouseOverTooltipsBackgroundColor" : "white",
"SNPMouseOverTooltipsBorderStyle" : "solid",
"SNPMouseOverTooltipsBorderWidth" : 0,
"SNPMouseOverTooltipsPadding" : "3px",
"SNPMouseOverTooltipsBorderRadius" : "3px",
"SNPMouseOverTooltipsOpacity" : 0.8,
"TEXTModuleDragEvent" : true,
"LINKMouseEvent" : true,
"LINKMouseClickDisplay" : false,
"LINKMouseClickOpacity" : 1.0,
"LINKMouseClickStrokeColor" : "green",
"LINKMouseClickStrokeWidth" : 4,
"LINKMouseDownDisplay" : false,
"LINKMouseDownOpacity" : 1.0,
"LINKMouseDownStrokeColor" : "#F26223",
"LINKMouseDownStrokeWidth" : 4,
"LINKMouseEnterDisplay" : false,
"LINKMouseEnterOpacity" : 1.0,
"LINKMouseEnterStrokeColor" : "#F26223",
"LINKMouseEnterStrokeWidth" : 4,
"LINKMouseLeaveDisplay" : false,
"LINKMouseLeaveOpacity" : 1.0,
"LINKMouseLeaveStrokeColor" : "#F26223",
"LINKMouseLeaveStrokeWidth" : 4,
"LINKMouseMoveDisplay" : false,
"LINKMouseMoveOpacity" : 1.0,
"LINKMouseMoveStrokeColor" : "#F26223",
"LINKMouseMoveStrokeWidth" : 4,
"LINKMouseOutDisplay" : false,
"LINKMouseOutAnimationTime" : 500,
"LINKMouseOutOpacity" : 1.0,
"LINKMouseOutStrokeColor" : "red",
"LINKMouseOutStrokeWidth" : 4,
"LINKMouseUpDisplay" : false,
"LINKMouseUpOpacity" : 1.0,
"LINKMouseUpStrokeColor" : "#F26223",
"LINKMouseUpStrokeWidth" : 4,
"LINKMouseOverDisplay" : false,
"LINKMouseOverOpacity" : 1.0,
"LINKMouseOverStrokeColor" : "#F26223",
"LINKMouseOverStrokeWidth" : 3,
"LINKMouseOverTooltipsHtml01" : "Link : ",
"LINKMouseOverTooltipsHtml02" : "",
"LINKMouseOverTooltipsPosition" : "absolute",
"LINKMouseOverTooltipsBackgroundColor" : "white",
"LINKMouseOverTooltipsBorderStyle" : "solid",
"LINKMouseOverTooltipsBorderWidth" : 0,
"LINKMouseOverTooltipsPadding" : "3px",
"LINKMouseOverTooltipsBorderRadius" : "3px",
"LINKMouseOverTooltipsOpacity" : 0.8,
"LINKLabelDragEvent" : false,
"HISTOGRAMMouseEvent" : true,
"HISTOGRAMMouseClickDisplay" : false,
"HISTOGRAMMouseClickColor" : "red", //"none","red"
"HISTOGRAMMouseClickOpacity" : 1.0, //"none",1.0
"HISTOGRAMMouseClickStrokeColor" : "none", //"none","#F26223"
"HISTOGRAMMouseClickStrokeWidth" : "none", //"none",3
"HISTOGRAMMouseDownDisplay" : false,
"HISTOGRAMMouseDownColor" : "red", //"none","red"
"HISTOGRAMMouseDownOpacity" : 1.0, //"none",1.0
"HISTOGRAMMouseDownStrokeColor" : "none", //"none","#F26223"
"HISTOGRAMMouseDownStrokeWidth" : "none", //"none",3
"HISTOGRAMMouseEnterDisplay" : false,
"HISTOGRAMMouseEnterColor" : "red", //"none","red"
"HISTOGRAMMouseEnterOpacity" : 1.0, //"none",1.0
"HISTOGRAMMouseEnterStrokeColor" : "none", //"none","#F26223"
"HISTOGRAMMouseEnterStrokeWidth" : "none", //"none",3
"HISTOGRAMMouseLeaveDisplay" : false,
"HISTOGRAMMouseLeaveColor" : "red", //"none","red"
"HISTOGRAMMouseLeaveOpacity" : 1.0, //"none",1.0
"HISTOGRAMMouseLeaveStrokeColor" : "none", //"none","#F26223"
"HISTOGRAMMouseLeaveStrokeWidth" : "none", //"none",3
"HISTOGRAMMouseMoveDisplay" : false,
"HISTOGRAMMouseMoveColor" : "red", //"none","red"
"HISTOGRAMMouseMoveOpacity" : 1.0, //"none",1.0
"HISTOGRAMMouseMoveStrokeColor" : "none", //"none","#F26223"
"HISTOGRAMMouseMoveStrokeWidth" : "none", //"none",3
"HISTOGRAMMouseOutDisplay" : false,
"HISTOGRAMMouseOutAnimationTime" : 500,
"HISTOGRAMMouseOutColor" : "red", //"none","red"
"HISTOGRAMMouseOutOpacity" : 1.0, //"none",1.0
"HISTOGRAMMouseOutStrokeColor" : "none", //"none","#F26223"
"HISTOGRAMMouseOutStrokeWidth" : "none", //"none",3
"HISTOGRAMMouseUpDisplay" : false,
"HISTOGRAMMouseUpColor" : "red", //"none","red"
"HISTOGRAMMouseUpOpacity" : 1.0, //"none",1.0
"HISTOGRAMMouseUpStrokeColor" : "none", //"none","#F26223"
"HISTOGRAMMouseUpStrokeWidth" : "none", //"none",3
"HISTOGRAMMouseOverDisplay" : false,
"HISTOGRAMMouseOverColor" : "red", //"none","red"
"HISTOGRAMMouseOverOpacity" : 1.0, //"none",1.0
"HISTOGRAMMouseOverStrokeColor" : "none", //"none","#F26223"
"HISTOGRAMMouseOverStrokeWidth" : "none", //"none",3
"HISTOGRAMMouseOverTooltipsHtml01" : "chr :",
"HISTOGRAMMouseOverTooltipsHtml02" : "<br>position: ",
"HISTOGRAMMouseOverTooltipsHtml03" : "-",
"HISTOGRAMMouseOverTooltipsHtml04" : "<br>name : ",
"HISTOGRAMMouseOverTooltipsHtml05" : "<br>value : ",
"HISTOGRAMMouseOverTooltipsHtml06" : "",
"HISTOGRAMMouseOverTooltipsPosition" : "absolute",
"HISTOGRAMMouseOverTooltipsBackgroundColor" : "white",
"HISTOGRAMMouseOverTooltipsBorderStyle" : "solid",
"HISTOGRAMMouseOverTooltipsBorderWidth" : 0,
"HISTOGRAMMouseOverTooltipsPadding" : "3px",
"HISTOGRAMMouseOverTooltipsBorderRadius" : "3px",
"HISTOGRAMMouseOverTooltipsOpacity" : 0.8,
"LINEMouseEvent" : true,
"LINEMouseClickDisplay" : false,
"LINEMouseClickLineOpacity" : 1, //"none"
"LINEMouseClickLineStrokeColor" : "red", //"none"
"LINEMouseClickLineStrokeWidth" : "none", //"none"
"LINEMouseDownDisplay" : false,
"LINEMouseDownLineOpacity" : 1, //"none"
"LINEMouseDownLineStrokeColor" : "red", //"none"
"LINEMouseDownLineStrokeWidth" : "none", //"none"
"LINEMouseEnterDisplay" : false,
"LINEMouseEnterLineOpacity" : 1, //"none"
"LINEMouseEnterLineStrokeColor" : "red", //"none"
"LINEMouseEnterLineStrokeWidth" : "none", //"none"
"LINEMouseLeaveDisplay" : false,
"LINEMouseLeaveLineOpacity" : 1, //"none"
"LINEMouseLeaveLineStrokeColor" : "red", //"none"
"LINEMouseLeaveLineStrokeWidth" : "none", //"none"
"LINEMouseMoveDisplay" : false,
"LINEMouseMoveLineOpacity" : 1, //"none"
"LINEMouseMoveLineStrokeColor" : "red", //"none"
"LINEMouseMoveLineStrokeWidth" : "none", //"none"
"LINEMouseOutDisplay" : false,
"LINEMouseOutAnimationTime" : 500,
"LINEMouseOutLineOpacity" : 1.0, //"none"
"LINEMouseOutLineStrokeColor" : "red", //"none"
"LINEMouseOutLineStrokeWidth" : "none", //"none"
"LINEMouseUpDisplay" : false,
"LINEMouseUpLineOpacity" : 1, //"none"
"LINEMouseUpLineStrokeColor" : "red", //"none"
"LINEMouseUpLineStrokeWidth" : "none", //"none"
"LINEMouseOverDisplay" : false,
"LINEMouseOverLineOpacity" : 1, //"none"
"LINEMouseOverLineStrokeColor" : "red", //"none"
"LINEMouseOverLineStrokeWidth" : "none", //"none"
"LINEMouseOverTooltipsHtml01" : "Line",
"LINEMouseOverTooltipsPosition" : "absolute",
"LINEMouseOverTooltipsBackgroundColor" : "white",
"LINEMouseOverTooltipsBorderStyle" : "solid",
"LINEMouseOverTooltipsBorderWidth" : 0,
"LINEMouseOverTooltipsPadding" : "3px",
"LINEMouseOverTooltipsBorderRadius" : "3px",
"LINEMouseOverTooltipsOpacity" : 0.8,
"SCATTERMouseEvent" : true,
"SCATTERMouseClickDisplay" : false,
"SCATTERMouseClickColor" : "red",
"SCATTERMouseClickCircleSize" : 4,
"SCATTERMouseClickCircleOpacity" : 1.0,
"SCATTERMouseClickCircleStrokeColor" : "#F26223",
"SCATTERMouseClickCircleStrokeWidth" : 0,
"SCATTERMouseClickTextFromData" : "fourth", //first,second,third,fourth column
"SCATTERMouseClickTextOpacity" : 1,
"SCATTERMouseClickTextColor" : "red",
"SCATTERMouseClickTextSize" : 8,
"SCATTERMouseClickTextPostionX" : 1.0,
"SCATTERMouseClickTextPostionY" : 10.0,
"SCATTERMouseClickTextDrag" : true,
"SCATTERMouseDownDisplay" : false,
"SCATTERMouseDownColor" : "green",
"SCATTERMouseDownCircleSize" : 4,
"SCATTERMouseDownCircleOpacity" : 1.0,
"SCATTERMouseDownCircleStrokeColor" : "#F26223",
"SCATTERMouseDownCircleStrokeWidth" : 0,
"SCATTERMouseEnterDisplay" : false,
"SCATTERMouseEnterColor" : "yellow",
"SCATTERMouseEnterCircleSize" : 4,
"SCATTERMouseEnterCircleOpacity" : 1.0,
"SCATTERMouseEnterCircleStrokeColor" : "#F26223",
"SCATTERMouseEnterCircleStrokeWidth" : 0,
"SCATTERMouseLeaveDisplay" : false,
"SCATTERMouseLeaveColor" : "pink",
"SCATTERMouseLeaveCircleSize" : 4,
"SCATTERMouseLeaveCircleOpacity" : 1.0,
"SCATTERMouseLeaveCircleStrokeColor" : "#F26223",
"SCATTERMouseLeaveCircleStrokeWidth" : 0,
"SCATTERMouseMoveDisplay" : false,
"SCATTERMouseMoveColor" : "red",
"SCATTERMouseMoveCircleSize" : 2,
"SCATTERMouseMoveCircleOpacity" : 1.0,
"SCATTERMouseMoveCircleStrokeColor" : "#F26223",
"SCATTERMouseMoveCircleStrokeWidth" : 0,
"SCATTERMouseOutDisplay" : false,
"SCATTERMouseOutAnimationTime" : 500,
"SCATTERMouseOutColor" : "red",
"SCATTERMouseOutCircleSize" : 2,
"SCATTERMouseOutCircleOpacity" : 1.0,
"SCATTERMouseOutCircleStrokeColor" : "red",
"SCATTERMouseOutCircleStrokeWidth" : 0,
"SCATTERMouseUpDisplay" : false,
"SCATTERMouseUpColor" : "grey",
"SCATTERMouseUpCircleSize" : 4,
"SCATTERMouseUpCircleOpacity" : 1.0,
"SCATTERMouseUpCircleStrokeColor" : "#F26223",
"SCATTERMouseUpCircleStrokeWidth" : 0,
"SCATTERMouseOverDisplay" : false,
"SCATTERMouseOverColor" : "red",
"SCATTERMouseOverCircleSize" : 2,
"SCATTERMouseOverCircleOpacity" : 1.0,
"SCATTERMouseOverCircleStrokeColor" : "#F26223",
"SCATTERMouseOverCircleStrokeWidth" : 3,
"SCATTERMouseOverTooltipsHtml01" : "item : ",
"SCATTERMouseOverTooltipsHtml02" : "<br>start : ",
"SCATTERMouseOverTooltipsHtml03" : "<br>end : ",
"SCATTERMouseOverTooltipsHtml04" : "<br>name : ",
"SCATTERMouseOverTooltipsHtml05" : "<br>des : ",
"SCATTERMouseOverTooltipsHtml06" : "",
"SCATTERMouseOverTooltipsPosition" : "absolute",
"SCATTERMouseOverTooltipsBackgroundColor" : "white",
"SCATTERMouseOverTooltipsBorderStyle" : "solid",
"SCATTERMouseOverTooltipsBorderWidth" : 0,
"SCATTERMouseOverTooltipsPadding" : "3px",
"SCATTERMouseOverTooltipsBorderRadius" : "3px",
"SCATTERMouseOverTooltipsOpacity" : 0.8,
"ARCMouseEvent" : true,
"ARCMouseClickDisplay" : false,
"ARCMouseClickColor" : "red",
"ARCMouseClickArcOpacity" : 1.0,
"ARCMouseClickArcStrokeColor" : "#F26223",
"ARCMouseClickArcStrokeWidth" : 1,
"ARCMouseClickTextFromData" : "fourth", //first,second,third,fourth column
"ARCMouseClickTextOpacity" : 1,
"ARCMouseClickTextColor" : "red",
"ARCMouseClickTextSize" : 8,
"ARCMouseClickTextPostionX" : 0,
"ARCMouseClickTextPostionY" : 0,
"ARCMouseClickTextDrag" : true,
"ARCMouseDownDisplay" : false,
"ARCMouseDownColor" : "green",
"ARCMouseDownArcOpacity" : 1.0,
"ARCMouseDownArcStrokeColor" : "#F26223",
"ARCMouseDownArcStrokeWidth" : 0,
"ARCMouseEnterDisplay" : false,
"ARCMouseEnterColor" : "yellow",
"ARCMouseEnterArcOpacity" : 1.0,
"ARCMouseEnterArcStrokeColor" : "#F26223",
"ARCMouseEnterArcStrokeWidth" : 0,
"ARCMouseLeaveDisplay" : false,
"ARCMouseLeaveColor" : "pink",
"ARCMouseLeaveArcOpacity" : 1.0,
"ARCMouseLeaveArcStrokeColor" : "#F26223",
"ARCMouseLeaveArcStrokeWidth" : 0,
"ARCMouseMoveDisplay" : false,
"ARCMouseMoveColor" : "red",
"ARCMouseMoveArcOpacity" : 1.0,
"ARCMouseMoveArcStrokeColor" : "#F26223",
"ARCMouseMoveArcStrokeWidth" : 0,
"ARCMouseOutDisplay" : false,
"ARCMouseOutAnimationTime" : 500,
"ARCMouseOutColor" : "red",
"ARCMouseOutArcOpacity" : 1.0,
"ARCMouseOutArcStrokeColor" : "red",
"ARCMouseOutArcStrokeWidth" : 0,
"ARCMouseUpDisplay" : false,
"ARCMouseUpColor" : "grey",
"ARCMouseUpArcOpacity" : 1.0,
"ARCMouseUpArcStrokeColor" : "#F26223",
"ARCMouseUpArcStrokeWidth" : 0,
"ARCMouseOverDisplay" : false,
"ARCMouseOverColor" : "red",
"ARCMouseOverArcOpacity" : 1.0,
"ARCMouseOverArcStrokeColor" : "#F26223",
"ARCMouseOverArcStrokeWidth" : 3,
"ARCMouseOverTooltipsHtml01" : "item : ",
"ARCMouseOverTooltipsHtml02" : "<br>start : ",
"ARCMouseOverTooltipsHtml03" : "<br>end : ",
"ARCMouseOverTooltipsHtml04" : "<br>des : ",
"ARCMouseOverTooltipsHtml05" : "",
"ARCMouseOverTooltipsPosition" : "absolute",
"ARCMouseOverTooltipsBackgroundColor" : "white",
"ARCMouseOverTooltipsBorderStyle" : "solid",
"ARCMouseOverTooltipsBorderWidth" : 0,
"ARCMouseOverTooltipsPadding" : "3px",
"ARCMouseOverTooltipsBorderRadius" : "3px",
"ARCMouseOverTooltipsOpacity" : 0.8,
"genomeBorder" : {
"display" : true,
"borderColor" : "#000",
"borderSize" : 0.5
},
"ticks" : {
"display" : true,
"len" : 5,
"color" : "#000",
"textSize" : 10,
"textColor" : "#000",
"scale" : 30000000
},
"genomeLabel" : {
"display" : true,
"textSize" : 15,
"textColor" : "#000",
"dx" : 0.028,
"dy" : "-0.55em"
}
};
self.CNVsettings = {
"maxRadius": 200,
"minRadius": 190,
"CNVwidth": 10,
"CNVColor": "#CAE1FF"
};
self.HEATMAPsettings = {
"innerRadius": -100,
"outerRadius": -100,
"maxColor": "red",
"minColor": "green"
};
self.SNPsettings = {
"maxRadius": 200,
"minRadius": 190,
"SNPFillColor": "red",
"PointType": "circle", //circle,rect
"circleSize": 2,
"rectWidth": 2,
"rectHeight": 2,
"SNPAnimationDisplay": false,
"SNPAnimationTime": 2000,
"SNPAnimationDelay": 20,
"SNPAnimationType": "bounce", //linear,circle,elastic,bounce
};
self.LINKsettings = {
"LinkRadius": 108,
"LinkFillColor": "red",
"LinkWidth": 3,
"displayLinkAxis": true,
"LinkAxisColor": "#B8B8B8",
"LinkAxisWidth": 0.5,
"LinkAxisPad": 3,
"displayLinkLabel": true,
"LinkLabelColor": "red",
"LinkLabelSize": 13,
"LinkLabelPad": 8
};
self.HISTOGRAMsettings = {
"maxRadius": 108,
"minRadius": 95,
"histogramFillColor": "red"
};
self.LINEsettings = {
"maxRadius": 108,
"minRadius": 95,
"LineFillColor": "red",
"LineWidth": 0.5
};
self.SCATTERsettings = {
"SCATTERRadius": 140,
"innerCircleSize": 1,
"outerCircleSize": 5,
"innerCircleColor": "#F26223",
"outerCircleColor": "#F26223",
"innerPointType": "circle", //circle,rect
"outerPointType": "circle", //circle,rect
"innerrectWidth": 2,
"innerrectHeight": 2,
"outerrectWidth": 2,
"outerrectHeight": 2,
"outerCircleOpacity": 1,
"random_data": 0,
"SCATTERAnimationDisplay": false,
"SCATTERAnimationTime": 2000,
"SCATTERAnimationDelay": 20,
"SCATTERAnimationType": "bounce", //linear,circle,elastic,bounce
};
self.BACKGROUNDsettings = {
"BginnerRadius": 180,
"BgouterRadius": 230,
"BgFillColor": "none",
"BgborderColor": "#000",
"BgborderSize" : 0.5,
"axisShow": "false",
"axisWidth": 0.3,
"axisColor": "#000",
"axisOpacity": 0.5,
"axisNum": 4
};
self.TEXTsettings = {
"x": 20,
"y": 20,
"textSize": 10,
"textWeight": "normal", //normal,bold,bolder,lighter,100,200,300,400,500,600,700,800,900
"textColor": "#000",
"textOpacity": 1.0
};
self.ARCsettings = {
"innerRadius": -30,
"outerRadius": -30
};
self.update_settings(self.argumentsBiocircosSettings)
self.target = "#" + self.settings.target;
self.svgWidth = self.settings.svgWidth;
self.svgHeight = self.settings.svgHeight;
self.chrPad = self.settings.chrPad;
self.innerRadius = self.settings.innerRadius;
self.outerRadius = self.settings.outerRadius;
self.zoom = self.settings.zoom;
self.testTip = self.settings.testTip;
self.genomeFillColor = self.settings.genomeFillColor;
self.genomeBorderDisplay=self.settings.genomeBorder.display;
self.genomeBorderColor=self.settings.genomeBorder.borderColor;
self.genomeBorderSize=self.settings.genomeBorder.borderSize;
self.genome = self.argumentsBiocircosGenome;
self.genome_matrix(self.argumentsBiocircosGenome)
self.ticksDisplay=self.settings.ticks.display;
self.ticksLength=self.settings.ticks.len;
self.ticksColor=self.settings.ticks.color;
self.ticksTextSize=self.settings.ticks.textSize;
self.ticksTextColor=self.settings.ticks.textColor;
self.ticksScale=self.settings.ticks.scale;
self.genomeTextDisplay=self.settings.genomeLabel.display;
self.genomeTextSize=self.settings.genomeLabel.textSize;
self.genomeTextColor=self.settings.genomeLabel.textColor;
self.genomeTextDx=self.settings.genomeLabel.dx;
self.genomeTextDy=self.settings.genomeLabel.dy;
var labeli= self.genomeLabel.length;
var initGenome = new Object();
for(var labelk=0;labelk<labeli;labelk++){
var labelInit=self.genomeLabel[labelk];
initGenome[labelInit]=labelk;
}
self.initGenome = initGenome;
}
BioCircos.prototype.update_settings = function(settings_object){
var self = this;
$.extend(self.settings, settings_object);
}
BioCircos.prototype.update_CNVsettings = function(settings_object){
var self = this;
$.extend(self.CNVsettings, settings_object);
}
BioCircos.prototype.update_HEATMAPsettings = function(settings_object){
var self = this;
$.extend(self.HEATMAPsettings, settings_object);
}
BioCircos.prototype.update_SNPsettings = function(settings_object){
var self = this;
$.extend(self.SNPsettings, settings_object);
}
BioCircos.prototype.update_LINKsettings = function(settings_object){
var self = this;
$.extend(self.LINKsettings, settings_object);
}
BioCircos.prototype.update_HISTOGRAMsettings = function(settings_object){
var self = this;
$.extend(self.HISTOGRAMsettings, settings_object);
}
BioCircos.prototype.update_LINEsettings = function(settings_object){
var self = this;
$.extend(self.LINEsettings, settings_object);
}
BioCircos.prototype.update_SCATTERsettings = function(settings_object){
var self = this;
$.extend(self.SCATTERsettings, settings_object);
}
BioCircos.prototype.update_BACKGROUNDsettings = function(settings_object){
var self = this;
$.extend(self.BACKGROUNDsettings, settings_object);
}
BioCircos.prototype.update_TEXTsettings = function(settings_object){
var self = this;
$.extend(self.TEXTsettings, settings_object);
}
BioCircos.prototype.update_ARCsettings = function(settings_object){
var self = this;
$.extend(self.ARCsettings, settings_object);
}
BioCircos.prototype.init_CNVsettings = function(){
var self = this;
self.CNVsettings = {
"maxRadius": 200,
"minRadius": 190,
"CNVwidth": 10,
"CNVColor": "#CAE1FF"
};
}
BioCircos.prototype.init_HEATMAPsettings = function(){
var self = this;
self.HEATMAPsettings = {
"innerRadius": -100,
"outerRadius": -100,
"maxColor": "red",
"minColor": "green"
};
}
BioCircos.prototype.init_SNPsettings = function(){
var self = this;
self.SNPsettings = {
"maxRadius": 200,
"minRadius": 190,
"SNPFillColor": "red",
"PointType": "circle",
"circleSize": 2,
"rectWidth": 2,
"rectHeight": 2,
"SNPAnimationDisplay": false,
"SNPAnimationTime": 2000,
"SNPAnimationDelay": 20,
"SNPAnimationType": "bounce", //linear,circle,elastic,bounce
};
}
BioCircos.prototype.init_LINKsettings = function(){
var self = this;
self.LINKsettings = {
"LinkRadius": 108,
"LinkFillColor": "red",
"LinkWidth": 3,
"displayLinkAxis": true,
"LinkAxisColor": "#B8B8B8",
"LinkAxisWidth": 0.5,
"LinkAxisPad": 3,
"displayLinkLabel": true,
"LinkLabelColor": "red",
"LinkLabelSize": 13,
"LinkLabelPad": 8
};
}
BioCircos.prototype.init_HISTOGRAMsettings = function(){
var self = this;
self.HISTOGRAMsettings = {
"maxRadius": 108,
"minRadius": 95,
"histogramFillColor": "red"
};
}
BioCircos.prototype.init_LINEsettings = function(){
var self = this;
self.LINEsettings = {
"maxRadius": 108,
"minRadius": 95,
"LineFillColor": "red",
"LineWidth": 0.5
};
}
BioCircos.prototype.init_SCATTERsettings = function(){
var self = this;
self.SCATTERsettings = {
"SCATTERRadius": 140,
"innerCircleSize": 1,
"outerCircleSize": 5,
"innerCircleColor": "#F26223",
"outerCircleColor": "#F26223",
"innerPointType": "circle", //circle,rect
"outerPointType": "circle", //circle,rect
"innerrectWidth": 2,
"innerrectHeight": 2,
"outerrectWidth": 2,
"outerrectHeight": 2,
"outerCircleOpacity": 1,
"random_data": 0,
"SCATTERAnimationDisplay": false,
"SCATTERAnimationTime": 2000,
"SCATTERAnimationDelay": 20,
"SCATTERAnimationType": "bounce", //linear,circle,elastic,bounce
};
}
BioCircos.prototype.init_BACKGROUNDsettings = function(){
var self = this;
self.BACKGROUNDsettings = {
"BginnerRadius": 180,
"BgouterRadius": 230,
"BgFillColor": "none",
"BgborderColor": "#000",
"BgborderSize" : 0.5,
"axisShow": "false",
"axisWidth": 0.3,
"axisColor": "#000",
"axisOpacity": 0.5,
"axisNum": 4
};
}
BioCircos.prototype.init_TEXTsettings = function(){
var self = this;
self.TEXTsettings = {
"x": 20,
"y": 20,
"textSize": 10,
"textColor": "#000",
"textWeight": "normal", //normal,bold,bolder,lighter,100,200,300,400,500,600,700,800,900
"textOpacity": 1.0
};
}
BioCircos.prototype.init_ARCsettings = function(){
var self = this;
self.ARCsettings = {
"innerRadius": -100,
"outerRadius": -100
};
}
BioCircos.prototype.genome_matrix = function(genome){
var self = this;
var i=self.genome.length;
var genomeLabel = new Array();
var genomeLength = new Array();
for(var k=0;k<i;k++){
genomeLabel[k]=self.genome[k][0];
}
for(var k=0;k<i;k++){
genomeLength[k]=self.genome[k][1];
}
var i=genomeLength.length;
var p=genomeLength.length;
var genome = new Array();
for(var k=0;k<i;k++){
genome[k]=new Array();
for(var j=0;j<p;j++){
genome[k][j]=0;
}
}
for(var k=0;k<i;k++){
genome[k][0]=genomeLength[k];
}
self.genomeLabel = genomeLabel;
self.genomeLength = genome;
}
BioCircos.prototype.heatmap_value_maxmin = function(heatmapIn){
var self = this;
var i=heatmapIn.length;
var heatmapValueList = new Array();
for(var k=0;k<i;k++){
heatmapValueList[k]=heatmapIn[k].value;
}
Array.max=function(array){
return Math.max.apply(Math,array);
}
Array.min=function(array){