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1945 lines (1694 loc) · 81.6 KB
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<!DOCTYPE html>
<html>
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<body data-spy="scroll" data-target="#navbar" data-offset="100">
<div class="header">
<div id="header_title"><button class="w3-button w3-xlarge" onclick="w3_open()">☰</button><a href="https://github.com/nilesh-tawari/ChronQC" target="_blank">ChronQC</a> Germline Plots</div>
<div id="report">Report generated on 2017-07-13</div>
</div>
<div class="w3-sidebar w3-bar-block " id="mySidebar">
<div id="mySidebar-2" class="summary" class="collapse" ><button class="w3-bar-item w3-button w3-large" onclick="w3_close()"><h2 style="font-size: 150%; ">« Plots</h2></button>
<div id="titles">
<nav id="navbar" class="navbar">
<ul class="nav" role="tablist">
<li class="nav-item">
<a href="#g1">Fastqc Percent Duplicates (Mean per run with past 1 year runs rolling mean and ±2 standard deviation)</a>
</li>
<li class="nav-item">
<a href="#g2">Fastqc % GC Content (Mean per run with past 1 year runs rolling mean and ±2 standard deviation)</a>
</li>
<li class="nav-item">
<a href="#g3">Fastqc Total Sequences (Mean per run with past 1 year runs rolling mean and ±2 standard deviation)</a>
</li>
<li class="nav-item">
<a href="#g4">Bcftools Stats Number Of Snps Monthly Box-and-Whisker Plot</a>
</li>
<li class="nav-item">
<a href="#g5">Bcftools Stats Number Of Indels Monthly Box-and-Whisker Plot</a>
</li>
<li class="nav-item">
<a href="#g6">Bcftools Stats Ts/Tv</a>
</li>
<li class="nav-item">
<a href="#g7">Qualimap Median Coverage</a>
</li>
<li class="nav-item">
<a href="#g8">% Samples per run with Qualimap Median Coverage ≥ 100</a>
</li>
</ul>
</nav>
</div>
</div>
</div>
<div id="main" >
<div class="exann">
<b>Annotate by Date:</b>
<input readonly id="calendarButton" placeholder="YYYY-MM-DD" />
<input name="buttonExecute" onclick="makeDateQuery(document.getElementById('calendarButton').value)" type="button" value="submit" />
<br/><br/><input type=checkbox checked id='chk-zoom' onChange='syncchk()'><label for='chk-zoom'>Synchronize Zoom</label>
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<h2 id="g1"></h2>
<div class="bigcontainer">
<div class="smallcontainer">
<div id="g1_divname" class = "chart"></div>
<div class="interaction"><br/><br/><b> Highlight Date Range:</b>
<input readonly id="g1_fromdate" placeholder="from" size="10"/><b>:</b><input readonly id="g1_todate" placeholder="until" size="10"/>
<input name="buttonExecute" onclick="Highlight(document.getElementById('g1_fromdate').value,document.getElementById('g1_todate').value,g1_graphvar)" type="button" value="submit" />
<button id = "g1_restorebutton" class="buttons">All historical data</button>
<button id = "g1_yearbutton" class="buttons">1 year data</button>
</div></div><div id="g1_labeldiv" class= "labels" ></div></div>
<h2 id="g2"></h2>
<div class="bigcontainer">
<div class="smallcontainer">
<div id="g2_divname" class = "chart"></div>
<div class="interaction"><br/><br/><b> Highlight Date Range:</b>
<input readonly id="g2_fromdate" placeholder="from" size="10"/><b>:</b><input readonly id="g2_todate" placeholder="until" size="10"/>
<input name="buttonExecute" onclick="Highlight(document.getElementById('g2_fromdate').value,document.getElementById('g2_todate').value,g2_graphvar)" type="button" value="submit" />
<button id = "g2_restorebutton" class="buttons">All historical data</button>
<button id = "g2_yearbutton" class="buttons">1 year data</button>
</div></div><div id="g2_labeldiv" class= "labels" ></div></div>
<h2 id="g3"></h2>
<div class="bigcontainer">
<div class="smallcontainer">
<div id="g3_divname" class = "chart"></div>
<div class="interaction"><br/><br/><b> Highlight Date Range:</b>
<input readonly id="g3_fromdate" placeholder="from" size="10"/><b>:</b><input readonly id="g3_todate" placeholder="until" size="10"/>
<input name="buttonExecute" onclick="Highlight(document.getElementById('g3_fromdate').value,document.getElementById('g3_todate').value,g3_graphvar)" type="button" value="submit" />
<button id = "g3_restorebutton" class="buttons">All historical data</button>
<button id = "g3_yearbutton" class="buttons">1 year data</button>
</div></div><div id="g3_labeldiv" class= "labels" ></div></div>
<h2 id="g4"></h2>
<div class="bigcontainer">
<div class="smallcontainer">
<div id="g4_divname" class = "chart"></div>
<div class="interaction"><br/><br/><b> Highlight Date Range:</b>
<input readonly id="g4_fromdate" placeholder="from" size="10"/><b>:</b><input readonly id="g4_todate" placeholder="until" size="10"/>
<input name="buttonExecute" onclick="Highlight(document.getElementById('g4_fromdate').value,document.getElementById('g4_todate').value,g4_graphvar)" type="button" value="submit" />
<button id = "g4_restorebutton" class="buttons">All historical data</button>
<button id = "g4_yearbutton" class="buttons">1 year data</button>
</div></div><div id="g4_labeldiv" class= "labels" ></div></div>
<h2 id="g5"></h2>
<div class="bigcontainer">
<div class="smallcontainer">
<div id="g5_divname" class = "chart"></div>
<div class="interaction"><br/><br/><b> Highlight Date Range:</b>
<input readonly id="g5_fromdate" placeholder="from" size="10"/><b>:</b><input readonly id="g5_todate" placeholder="until" size="10"/>
<input name="buttonExecute" onclick="Highlight(document.getElementById('g5_fromdate').value,document.getElementById('g5_todate').value,g5_graphvar)" type="button" value="submit" />
<button id = "g5_restorebutton" class="buttons">All historical data</button>
<button id = "g5_yearbutton" class="buttons">1 year data</button>
</div></div><div id="g5_labeldiv" class= "labels" ></div></div>
<h2 id="g6"></h2>
<div class="bigcontainer">
<div class="smallcontainer">
<div id="g6_divname" class = "chart"></div>
<div class="interaction"><br/><br/><b> Highlight Date Range:</b>
<input readonly id="g6_fromdate" placeholder="from" size="10"/><b>:</b><input readonly id="g6_todate" placeholder="until" size="10"/>
<input name="buttonExecute" onclick="Highlight(document.getElementById('g6_fromdate').value,document.getElementById('g6_todate').value,g6_graphvar)" type="button" value="submit" />
<button id = "g6_restorebutton" class="buttons">All historical data</button>
<button id = "g6_yearbutton" class="buttons">1 year data</button>
</div></div><div id="g6_labeldiv" class= "labels" ></div></div>
<h2 id="g7"></h2>
<div class="bigcontainer">
<div class="smallcontainer">
<div id="g7_divname" class = "chart"></div>
<div class="interaction"><br/><br/><b> Highlight Date Range:</b>
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<input name="buttonExecute" onclick="Highlight(document.getElementById('g7_fromdate').value,document.getElementById('g7_todate').value,g7_graphvar)" type="button" value="submit" />
<button id = "g7_restorebutton" class="buttons">All historical data</button>
<button id = "g7_yearbutton" class="buttons">1 year data</button>
</div></div><div id="g7_labeldiv" class= "labels" ></div></div>
<h2 id="g8"></h2>
<div class="bigcontainer">
<div class="smallcontainer">
<div id="g8_divname" class = "chart"></div>
<div class="interaction"><br/><br/><b> Highlight Date Range:</b>
<input readonly id="g8_fromdate" placeholder="from" size="10"/><b>:</b><input readonly id="g8_todate" placeholder="until" size="10"/>
<input name="buttonExecute" onclick="Highlight(document.getElementById('g8_fromdate').value,document.getElementById('g8_todate').value,g8_graphvar)" type="button" value="submit" />
<button id = "g8_restorebutton" class="buttons">All historical data</button>
<button id = "g8_yearbutton" class="buttons">1 year data</button>
</div></div><div id="g8_labeldiv" class= "labels" ></div></div>
</div>
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var elements =document.getElementsByClassName("bigcontainer");
for (var i = 0; i < elements.length; i++) {
elements[i].style.width="90%";
elements[i].style.zoom="100%";
}
for (var i = 0; i < gs.length; i++) {
gs[i].resize()
}
}
function w3_close() {
document.getElementById("mySidebar").style.display = "none";
document.getElementById("main").style.marginLeft = "-18em";
var elements =document.getElementsByClassName("bigcontainer");
for (var i = 0; i < elements.length; i++) {
elements[i].style.width="100%";
elements[i].style.zoom="100%";
}
//var elements =document.getElementsByClassName("chart");
//for (var i = 0; i < elements.length; i++) {
// elements[i].style.top=0;
//elements[i].style.right=0
//}
for (var i = 0; i < gs.length; i++) {
gs[i].resize()
}
}
////////////////////////////////////////////////////////////////////////////////////////
var $j = jQuery.noConflict();
////////////////////////////////////////////////////////////////////////////////////////
var panelname = "Germline";
var obj = [];
var runjson = '';
var runrequest= $j.ajax({ type: "GET",
url: "https://localhost:8000/runannotation",
async: false,
success : function(text){
runjson = text;
}
});
if(runjson.length==0){var obj = '';}
else {
var obj12 = JSON.parse(runjson);
for(i = 0; i < obj12.length; i++){
if (obj12[i].Panel==panelname){
obj.push(obj12[i]);
}
}
}
var datejson = '';
var dateobj = [];
var daterequest= $j.ajax({ type: "GET",
url: "https://localhost:8000/dateannotation",
async: false,
success : function(text){
datejson = text;
}
});
if(datejson.length==0){var dateobj = '' }
else {
var dateobj12 = JSON.parse(datejson);
for(i = 0; i < dateobj12.length; i++){
if (dateobj12[i].Panel==panelname){
dateobj12[i].Notes = dateobj12[i].Notes.replace(/hashmark/g, '#');
dateobj12[i].Notes = dateobj12[i].Notes.replace(/questmark/g, '?');
dateobj12[i].Notes = dateobj12[i].Notes.replace(/backslash/g, '/');
dateobj.push(dateobj12[i]);
}
}
}
///////////////////////////////////////////////////////////////////////////////////////
function makeQuery(Runname, date){
if (runrequest.status<600 && runrequest.status >=400 || runrequest.status ==0){
alert("Visit https://github.com/nilesh-tawari/ChronQC for details on using ChronQC.");
}
else{
var annotation = prompt("RunName: " + run , "Annotation");
if (annotation==null || annotation == "Annotation"){}
else{
var str = annotation;
var str = str.replace(/[?]/g, '?');
var str = str.replace(/[#]/g, '#');
var annotation = str.replace(/\//g, '⁄');
$j.get("https://localhost:8000/dataQuery/"+ Runname+ "/" + panelname +"/" + annotation, function(result){})
alert("Annotation Added!")
window.location.reload(true);
}
}
}
///////////////////////////////////////////////////////////////////////////////////////
function makeDateQuery(Date){
if (daterequest.status >=400 && daterequest.status<600 || daterequest.status ==0){
alert("Visit https://github.com/nilesh-tawari/ChronQC for details on using ChronQC.");
}
else{
var Notes = prompt("Date: " + Date , "Annotation (not more than 10 characters)");
if( Date==null || Notes == null || Notes == "Annotation (not more than 10 characters)"|| Notes == "Annotation"){ }
else if(Notes.length>10){alert("Annotation length must not exceed 10 characters")}
else{
var str = Notes;
var str = str.replace(/[?]/g, 'questmark');
var str = str.replace(/[#]/g, 'hashmark');
var Notes = str.replace(/\//g, 'backslash');
$j.get("https://localhost:8000/datedataQuery/"+ Date + "/" + panelname + "/" + Notes, function(result){})
alert("Annotation Added!")
window.location.reload(true);
}
}
}
////////////////////////////////////////////////////////////////////////////////////////
window.onload = function( ) {
Calendar.setup({dateField:'calendarButton',triggerElement : 'calendarButton'});
Calendar.setup({dateField:"g1_fromdate",triggerElement : "g1_fromdate"}); Calendar.setup({dateField:"g1_todate",triggerElement : "g1_todate"});
Calendar.setup({dateField:"g2_fromdate",triggerElement : "g2_fromdate"}); Calendar.setup({dateField:"g2_todate",triggerElement : "g2_todate"});
Calendar.setup({dateField:"g3_fromdate",triggerElement : "g3_fromdate"}); Calendar.setup({dateField:"g3_todate",triggerElement : "g3_todate"});
Calendar.setup({dateField:"g4_fromdate",triggerElement : "g4_fromdate"}); Calendar.setup({dateField:"g4_todate",triggerElement : "g4_todate"});
Calendar.setup({dateField:"g5_fromdate",triggerElement : "g5_fromdate"}); Calendar.setup({dateField:"g5_todate",triggerElement : "g5_todate"});
Calendar.setup({dateField:"g6_fromdate",triggerElement : "g6_fromdate"}); Calendar.setup({dateField:"g6_todate",triggerElement : "g6_todate"});
Calendar.setup({dateField:"g7_fromdate",triggerElement : "g7_fromdate"}); Calendar.setup({dateField:"g7_todate",triggerElement : "g7_todate"});
Calendar.setup({dateField:"g8_fromdate",triggerElement : "g8_fromdate"}); Calendar.setup({dateField:"g8_todate",triggerElement : "g8_todate"});
}
////////////////////////////////////////////////////////////////////////////////////////
function candlePlotter(e) {
if (e.seriesIndex !== 0) return;
var BAR_WIDTH = 60;
var prices = [];
var price;
var sets = e.allSeriesPoints;
for (var p = 0 ; p < sets[0].length; p++) {
price = {
open : sets[0][p].yval,
close : sets[1][p].yval,
high : sets[2][p].yval,
low : sets[3][p].yval,
middle: sets[4][p].yval,
out: sets[5][p].yval,
openY : sets[0][p].y,
closeY : sets[1][p].y,
highY : sets[2][p].y,
lowY : sets[3][p].y,
middleY : sets[4][p].y,
outY : sets[5][p].y
};
prices.push(price);
}
var area = e.plotArea;
var ctx = e.drawingContext;
ctx.strokeStyle = '#202020';
ctx.fillStyle="#ffffff";
ctx.lineWidth = 0.8;
for (p = 0 ; p < prices.length; p++) {
ctx.beginPath();
price = prices[p];
var topY = area.h * price.highY + area.y;
var midY = area.h * price.middleY + area.y;
var outlierY = area.h * price.outY + area.y;
var bottomY = area.h * price.lowY + area.y;
var centerX = area.x + sets[0][p].x * area.w;
var bodyY;
if (price.open > price.close) {
ctx.fillStyle ='#f2a104';
ctx.strokeStyle = "#bb1924";
bodyY = area.h * price.openY + area.y;
}
else {
ctx.fillStyle = '#ffd9b3';
ctx.strokeStyle = "#ffa64d";
ctx.lineWidth=1.5;
bodyY = area.h * price.closeY + area.y;
}
var bodyHeight = area.h * Math.abs(price.openY - price.closeY);
ctx.fillRect(centerX - BAR_WIDTH / 2, bodyY, BAR_WIDTH, bodyHeight);
ctx.strokeRect(centerX - BAR_WIDTH / 2, bodyY, BAR_WIDTH, bodyHeight);
ctx.moveTo(centerX, topY);
ctx.lineTo(centerX, bottomY);
ctx.moveTo(centerX - BAR_WIDTH / 2, midY);
ctx.lineTo(centerX + BAR_WIDTH / 2, midY);
ctx.closePath();
ctx.stroke();
ctx.fillStyle = "#ff6666";
ctx.arc(centerX, outlierY, 3, 0, Math.PI * 2);
ctx.fill();
}
}
////////////////////////////////////////////////////////////////////////////
function Highlight(highlight_start,highlight_end,a){
area = a.plotter_.area
ctx = a.hidden_ctx_
var start = new Date(highlight_start);
var end = new Date(highlight_end);
if(start>end){
alert("Wrong Date ('Until' date is later than 'From' date)")
return
}
else if(moment(start).format("DD/MM/YYYY") == moment(end).format("DD/MM/YYYY")){
alert("Wrong Date ('Until' date is equal to 'From' date)")
return
}
else{
var left = a.toDomXCoord(start);
var right = a.toDomXCoord(end);
ctx.beginPath();
ctx.fillStyle = "rgba(255, 255, 102, 0.5)";
ctx.fillRect(left, area.y, right - left, area.h);
}
};
////////////////////////////////////////////////////////////////////////
/*
function copyToClipboard(textToCopy){
$j("body")
.append($j('<input type="text" name="fname" class="textToCopyInput"/>' )
.val(textToCopy))
.find(".textToCopyInput")
.select();
if (textToCopy != null){
var successful = document.execCommand('copy');
var msg = successful ? 'successful' : 'unsuccessful';
} else {
return ;
}
$j(".textToCopyInput").remove();
}
*/
/////////////////////////////////////////////////////////////////////////////
function syncchk() {
var zoom = document.getElementById('chk-zoom').checked;
sync.detach();
sync = Dygraph.synchronize(gs, {
zoom: zoom,
selection: true,
range: false
});
}
/////////////////////////////////////////////////////////////////////////////////////////
function legendFormatter(data) {
if (data.x == null) {
return ' ';
}
var html = data.xHTML;
//console.log(data.series)
return html;
}
/////////////////////////////////////////////////////////////////////////////////////////
var gs = [];
/////////////////////////////////////////////////////////////////////////////////////////
g1_dataname = [[1475539200000,null,null,null,null],[1478217600000,null,51.75,null,51.75],[1478822400000,51.59,52.14,52.69,52.53],[1479427200000,51.47,52.97,54.47,54.64],[1480032000000,51.86,53.59,55.32,55.42],[1480550400000,52.22,53.77,55.32,54.5],[1481155200000,52.49,53.94,55.39,54.81],[1483315200000,52.6,53.93,55.26,53.83],[1483920000000,52.77,54.04,55.31,54.84],[1484524800000,52.6,53.88,55.16,52.57],[1485129600000,52.24,53.65,55.06,51.58],[1485734400000,51.91,53.43,54.95,51.24],[1486339200000,51.52,53.19,54.86,50.57],[1486944000000,51.6,53.2,54.8,53.35],[1487548800000,51.7,53.24,54.78,53.74],[1488153600000,51.56,53.12,54.68,51.37],[1488758400000,51.66,53.21,54.76,54.56],[1489363200000,51.75,53.33,54.91,55.24],[1489968000000,51.83,53.39,54.95,54.42],[1490572800000,51.91,53.5,55.09,55.49],[1491177600000,51.93,53.68,55.43,57.16],[1491782400000,51.99,53.7,55.41,53.99],[1492387200000,51.95,53.64,55.33,52.49],[1492992000000,52.01,53.66,55.31,54.15],[1495584000000,null,null,null,null]]
g1_runname = [[null,""],["Run-1",""],["Run-2",""],["Run-3",""],["Run-4",""],["Run-5",""],["Run-6",""],["Run-7",""],["Run-8",""],["Run-9",""],["Run-10",""],["Run-11",""],["Run-12",""],["Run-13",""],["Run-14",""],["Run-15",""],["Run-16",""],["Run-17",""],["Run-18",""],["Run-19",""],["Run-20",""],["Run-21",""],["Run-22",""],["Run-23",""],[null,""]]
g1_samplename = [null,"SampID_6737 (48.86), SampID_6738 (49.3), SampID_6740 (57.1)","SampID_6741 (51.68), SampID_6743 (54.58), SampID_6744 (51.33)","SampID_6320 (54.15), SampID_6321 (54.31), SampID_6319 (55.46)","SampID_11676 (56.0), SampID_11677 (54.77), SampID_11678 (55.48)","SampID_13726 (55.24), SampID_13727 (54.34), SampID_13728 (53.93)","SampID_10895 (55.56), SampID_10893 (54.5), SampID_10894 (54.38)","SampID_26782 (54.23), SampID_26783 (52.93), SampID_26784 (54.34)","SampID_26776 (55.34), SampID_26777 (55.59), SampID_26778 (53.6)","SampID_10896 (53.14), SampID_10897 (54.0), SampID_10898 (50.58)","SampID_10901 (53.51), SampID_10902 (50.34), SampID_10900 (50.9)","SampID_10903 (50.93), SampID_10904 (51.54)","SampID_6745 (51.33), SampID_6742 (52.62), SampID_6739 (47.76)","SampID_7170 (53.26), SampID_7173 (52.53), SampID_7176 (54.26)","SampID_7185 (53.88), SampID_7179 (52.74), SampID_7182 (54.6)","SampID_7171 (51.47), SampID_7174 (50.61), SampID_7177 (52.02)","SampID_7180 (54.11), SampID_7184 (55.97), SampID_7186 (53.61)","SampID_7187 (55.0), SampID_7188 (56.89), SampID_7191 (53.83)","SampID_7196 (54.11), SampID_7193 (54.72), SampID_7194 (54.44)","SampID_7199 (58.67), SampID_7198 (53.11), SampID_7197 (54.69)","SampID_7201 (55.9), SampID_7202 (58.42)","SampID_6312 (55.59), SampID_6316 (52.44), SampID_6317 (53.93)","SampID_6536 (52.02), SampID_6537 (51.69), SampID_6538 (53.75)","SampID_11686 (55.99), SampID_11657 (53.53), SampID_11687 (52.92)",null]
for (j = 0; j < g1_dataname.length; j++){
g1_dataname[j][0] = new Date(g1_dataname[j][0])
}
for (j = 0; j < g1_runname.length; j++){
for (i = 0; i < obj.length; i++){
var ann = obj[i]
if(ann.Run == g1_runname[j][0]){
g1_runname[j][1]=ann.Annotation
}else{}
}
}
g1_graphvar = new Dygraph(
document.getElementById("g1_divname"),
g1_dataname,
{
labels: [ "Date","Lower" , "Mean", "Upper", "Scatter"],
labelsDiv: document.getElementById("g1_labeldiv"),
labelsSeparateLines: true,
legend: "always",
title: 'Fastqc Percent Duplicates (Mean per run with past 1 year runs rolling mean and ±2 standard deviation)',
xlabel: 'Date',
ylabel: 'Fastqc Percent Duplicates (Mean per run)',
showRangeSelector: true,
rangeSelectorHeight: 20,
rangeSelectorPlotFillColor: "rgba(0,0,0,0)",
rangeSelectorPlotFillGradientColor: "rgba(0,0,0,0)",
rangeSelectorPlotStrokeColor: "rgba(0,0,0,0)",
highlightSeriesOpts: { highlightCircleSize : 5 },
interactionModel: Dygraph.defaultInteractionModel,
includeZero: true,
displayAnnotations: true,
drawHighlightPointCallback: Dygraph.Circles.HEXAGON,
axisLabelFontSize: 10,
titleHeight: 25,
xLabelHeight: 15,
yLabelWidth: 15,
legendFormatter: legendFormatter,
axes: {
x: {
valueFormatter: function me(d,opt,se,dy,row,col) {
var text = [],
data = g1_dataname[row],
run = g1_runname[row],
sample = g1_samplename[row];
text = "<b>Run Name: </b>".fontcolor("#800000") + run[col]
+ "<br/><b>Sample Name (y-value): </b>".fontcolor("#008080") + "<font size='-1.5'>" + sample + "</font>"
+ "<br><b>Date:</b> ".fontcolor("#800080") + moment(d).format("DD/MM/YYYY")
+ "<br/><b> Mean: </b>".fontcolor("#006400") + data[2]
+ "<br/><b> 2SD: </b>".fontcolor("#ff0000") + data[1] + ' - ' + data[3]
+ "<br/><b> Fastqc Percent Duplicates (Mean per run): </b>".fontcolor("#000080") + data[4]
+ '</font>'
if (run[1].length == 0){return text}
else if (run[1].length != 0) {
note = "<br/><b>Notes: </b><br/>" + run[1]
text = text + note.fontcolor("red")
return text
}
else {console.log("Error in labels")}
},
},
},
series: {
"Lower" : {
strokePattern: Dygraph.DASHED_LINE ,
color: "#ff0000",
strokeWidth: 2,
},
"Mean" : {
drawPoints: false,
color: "#006400",
strokeWidth: 2,
},
"Upper": {
strokePattern: Dygraph.DASHED_LINE ,
color: "#ff0000",
strokeWidth: 2,
},
"Scatter" : {
drawPoints: true,
color: "#0080ff",
pointSize: 3,
strokeWidth: 0,
}
},
underlayCallback: function(canvas, area, g) {
ctx = g.hidden_ctx_;
ctx.strokeStyle = "#dd4b39";
for (i = 0; i < g1_dataname.length; i++) {
var point = g1_dataname[i][4],
note = g1_runname[i][1],
date = g1_dataname[i][0];
if (g1_runname[i][0] == null){}
else if(note.length != 0){
mutated = g.toDomCoords(date, point)
ctx.beginPath();
ctx.arc(mutated[0], mutated[1],5,0,Math.PI*2,true);
ctx.closePath();
ctx.stroke();
}
}
ctx.fillStyle = "#0080ff";
ctx.strokeStyle = "#0080ff";
var [bottom,top] = g.yAxisRange();
for(i = 0; i < dateobj.length; i++) {
date = dateobj[i];
position = g.toDomCoords(date.Annotated_date,bottom);
dateobj[i].key3 = position;
canvas.fillText(dateobj[i].Notes,dateobj[i].key3[0]+2,dateobj[i].key3[1]-15);
canvas.strokeRect(dateobj[i].key3[0],dateobj[i].key3[1]-25,dateobj[i].Notes.length*7,15)
canvas.beginPath();
canvas.moveTo(dateobj[i].key3[0],dateobj[i].key3[1]);
canvas.lineTo(dateobj[i].key3[0],dateobj[i].key3[1]-10);
canvas.closePath();
canvas.stroke();
}
},
pointClickCallback: function(e, point) {
run = g1_runname[point.idx][0]
date = g1_dataname[point.idx][0]
date = moment(date).format("DD-MM-YYYY")
//copyToClipboard(run)
makeQuery(run,date)
},
}
);
document.getElementById("g1_restorebutton").onclick = function() { restorePositioning(g1_graphvar); };
document.getElementById("g1_yearbutton").onclick = function() {g1_graphvar.updateOptions({dateWindow: [Date.parse('2016-10-04'),Date.parse('2017-05-24 00:00:00')]});};
gs.push(g1_graphvar);
g2_dataname = [[1475539200000,null,null,null,null],[1478217600000,null,46.33,null,46.33],[1478822400000,45.93,46.16,46.39,46.0],[1479427200000,45.54,47.0,48.46,48.67],[1480032000000,44.95,46.5,48.05,45.0],[1480550400000,44.7,46.2,47.7,45.0],[1481155200000,43.8,45.67,47.54,43.0],[1483315200000,43.61,45.43,47.25,44.0],[1483920000000,43.49,45.25,47.01,44.0],[1484524800000,43.19,45.0,46.81,43.0],[1485129600000,42.98,44.8,46.62,43.0],[1485734400000,42.83,44.64,46.45,43.0],[1486339200000,42.98,44.75,46.52,46.0],[1486944000000,43.02,45.08,47.14,49.0],[1487548800000,43.07,45.4,47.73,49.67],[1488153600000,43.23,45.58,47.93,48.0],[1488758400000,43.36,45.81,48.26,49.33],[1489363200000,43.48,46.06,48.64,50.0],[1489968000000,43.62,46.24,48.86,49.33],[1490572800000,43.75,46.44,49.13,50.0],[1491177600000,43.88,46.59,49.3,49.5],[1491782400000,44.02,46.74,49.46,49.67],[1492387200000,44.14,46.84,49.54,49.0],[1492992000000,44.09,46.76,49.43,45.0],[1495584000000,null,null,null,null]]
g2_runname = [[null,""],["Run-1",""],["Run-2",""],["Run-3",""],["Run-4",""],["Run-5",""],["Run-6",""],["Run-7",""],["Run-8",""],["Run-9",""],["Run-10",""],["Run-11",""],["Run-12",""],["Run-13",""],["Run-14",""],["Run-15",""],["Run-16",""],["Run-17",""],["Run-18",""],["Run-19",""],["Run-20",""],["Run-21",""],["Run-22",""],["Run-23",""],[null,""]]
g2_samplename = [null,"SampID_6737 (46.0), SampID_6738 (45.0), SampID_6740 (48.0)","SampID_6741 (46.0), SampID_6743 (46.0), SampID_6744 (46.0)","SampID_6320 (49.0), SampID_6321 (48.0), SampID_6319 (49.0)","SampID_11676 (45.0), SampID_11677 (45.0), SampID_11678 (45.0)","SampID_13726 (45.0), SampID_13727 (45.0), SampID_13728 (45.0)","SampID_10895 (43.0), SampID_10893 (43.0), SampID_10894 (43.0)","SampID_26782 (44.0), SampID_26783 (44.0), SampID_26784 (44.0)","SampID_26776 (44.0), SampID_26777 (44.0), SampID_26778 (44.0)","SampID_10896 (43.0), SampID_10897 (43.0), SampID_10898 (43.0)","SampID_10901 (43.0), SampID_10902 (43.0), SampID_10900 (43.0)","SampID_10903 (43.0), SampID_10904 (43.0)","SampID_6745 (47.0), SampID_6742 (46.0), SampID_6739 (45.0)","SampID_7170 (49.0), SampID_7173 (49.0), SampID_7176 (49.0)","SampID_7185 (50.0), SampID_7179 (49.0), SampID_7182 (50.0)","SampID_7171 (48.0), SampID_7174 (48.0), SampID_7177 (48.0)","SampID_7180 (49.0), SampID_7184 (49.0), SampID_7186 (50.0)","SampID_7187 (50.0), SampID_7188 (50.0), SampID_7191 (50.0)","SampID_7196 (49.0), SampID_7193 (49.0), SampID_7194 (50.0)","SampID_7199 (50.0), SampID_7198 (50.0), SampID_7197 (50.0)","SampID_7201 (50.0), SampID_7202 (49.0)","SampID_6312 (50.0), SampID_6316 (50.0), SampID_6317 (49.0)","SampID_6536 (49.0), SampID_6537 (49.0), SampID_6538 (49.0)","SampID_11686 (45.0), SampID_11657 (45.0), SampID_11687 (45.0)",null]
for (j = 0; j < g2_dataname.length; j++){
g2_dataname[j][0] = new Date(g2_dataname[j][0])
}
for (j = 0; j < g2_runname.length; j++){
for (i = 0; i < obj.length; i++){
var ann = obj[i]
if(ann.Run == g2_runname[j][0]){
g2_runname[j][1]=ann.Annotation
}else{}
}
}
g2_graphvar = new Dygraph(
document.getElementById("g2_divname"),
g2_dataname,
{
labels: [ "Date","Lower" , "Mean", "Upper", "Scatter"],
labelsDiv: document.getElementById("g2_labeldiv"),
labelsSeparateLines: true,
legend: "always",
title: 'Fastqc % GC Content (Mean per run with past 1 year runs rolling mean and ±2 standard deviation)',
xlabel: 'Date',
ylabel: 'Fastqc % GC Content (Mean per run)',
showRangeSelector: true,
rangeSelectorHeight: 20,
rangeSelectorPlotFillColor: "rgba(0,0,0,0)",
rangeSelectorPlotFillGradientColor: "rgba(0,0,0,0)",
rangeSelectorPlotStrokeColor: "rgba(0,0,0,0)",
highlightSeriesOpts: { highlightCircleSize : 5 },
interactionModel: Dygraph.defaultInteractionModel,
includeZero: true,
displayAnnotations: true,
drawHighlightPointCallback: Dygraph.Circles.HEXAGON,
axisLabelFontSize: 10,
titleHeight: 25,
xLabelHeight: 15,
yLabelWidth: 15,
legendFormatter: legendFormatter,
axes: {
x: {
valueFormatter: function me(d,opt,se,dy,row,col) {
var text = [],
data = g2_dataname[row],
run = g2_runname[row],
sample = g2_samplename[row];
text = "<b>Run Name: </b>".fontcolor("#800000") + run[col]
+ "<br/><b>Sample Name (y-value): </b>".fontcolor("#008080") + "<font size='-1.5'>" + sample + "</font>"
+ "<br><b>Date:</b> ".fontcolor("#800080") + moment(d).format("DD/MM/YYYY")
+ "<br/><b> Mean: </b>".fontcolor("#006400") + data[2]
+ "<br/><b> 2SD: </b>".fontcolor("#ff0000") + data[1] + ' - ' + data[3]
+ "<br/><b> Fastqc % GC Content (Mean per run): </b>".fontcolor("#000080") + data[4]
+ '</font>'
if (run[1].length == 0){return text}
else if (run[1].length != 0) {
note = "<br/><b>Notes: </b><br/>" + run[1]
text = text + note.fontcolor("red")
return text
}
else {console.log("Error in labels")}
},
},
},
series: {
"Lower" : {
strokePattern: Dygraph.DASHED_LINE ,
color: "#ff0000",
strokeWidth: 2,
},
"Mean" : {
drawPoints: false,
color: "#006400",
strokeWidth: 2,
},
"Upper": {
strokePattern: Dygraph.DASHED_LINE ,
color: "#ff0000",
strokeWidth: 2,
},
"Scatter" : {
drawPoints: true,
color: "#0080ff",
pointSize: 3,
strokeWidth: 0,
}
},
underlayCallback: function(canvas, area, g) {
ctx = g.hidden_ctx_;
ctx.strokeStyle = "#dd4b39";
for (i = 0; i < g2_dataname.length; i++) {
var point = g2_dataname[i][4],
note = g2_runname[i][1],
date = g2_dataname[i][0];
if (g2_runname[i][0] == null){}
else if(note.length != 0){
mutated = g.toDomCoords(date, point)
ctx.beginPath();
ctx.arc(mutated[0], mutated[1],5,0,Math.PI*2,true);
ctx.closePath();
ctx.stroke();
}
}
ctx.fillStyle = "#0080ff";
ctx.strokeStyle = "#0080ff";
var [bottom,top] = g.yAxisRange();
for(i = 0; i < dateobj.length; i++) {
date = dateobj[i];
position = g.toDomCoords(date.Annotated_date,bottom);
dateobj[i].key3 = position;
canvas.fillText(dateobj[i].Notes,dateobj[i].key3[0]+2,dateobj[i].key3[1]-15);
canvas.strokeRect(dateobj[i].key3[0],dateobj[i].key3[1]-25,dateobj[i].Notes.length*7,15)
canvas.beginPath();
canvas.moveTo(dateobj[i].key3[0],dateobj[i].key3[1]);
canvas.lineTo(dateobj[i].key3[0],dateobj[i].key3[1]-10);
canvas.closePath();