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epiviz-igv-track.html
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epiviz-igv-track.html
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<!-- Polymer dependency -->
<link rel="import" href="bower_components/polymer/polymer-element.html">
<!-- Epiviz imports dependency -->
<!-- <link rel="import" href="bower_components/epiviz-imports/epiviz-common-js.html"> -->
<!-- IGV imports dependency -->
<script type="text/javascript" src="https://igv.org/web/release/1.0.9/igv-1.0.9.js"></script>
<link rel="stylesheet" type="text/css" href="https://igv.org/web/release/1.0.9/igv-1.0.9.css">
<!-- Polymer Elements dependency -->
<link rel="import" href="bower_components/paper-dialog/paper-dialog.html">
<link rel="import" href="bower_components/paper-button/paper-button.html">
<link rel="import" href="bower_components/paper-input/paper-input.html">
<link rel="import" href="bower_components/paper-dropdown-input/paper-dropdown-input.html">
<link rel="import" href="bower_components/paper-swatch-picker/paper-swatch-picker.html">
<link rel="import" href="bower_components/paper-styles/color.html">
<link rel="import" href="bower_components/paper-styles/typography.html">
<link rel="import" href="bower_components/iron-form/iron-form.html">
<!--
<h2> IGV Chart Component </h2>
-->
<dom-module id="epiviz-igv-track">
<template>
<style>
:host {
display: inline-block;
min-width: 250px;
}
#chart {
position: relative;
}
.tracks {
display: inline-block;
}
:host #igvControlDiv {
visibility: hidden;
display: none;
}
.igv-track-type-row {
padding: 10px;
border-bottom: 1px solid #E8E8E8;
}
[horizontal][layout] {
width: 400px;
display: flex;
flex-direction: row;
}
#trackSettings {
padding: 25px;
margin: 10px;
}
.fElement {
padding: 5px;
}
</style>
<!-- local DOM goes here -->
<div class="tracks">
<template id="dataTracks" is="dom-repeat" items={{tracks}}>
<button on-click="_editTrack">{{item.name}}</button>
</template>
</div>
<button on-click="_addTrack">Add New IGV Track</button>
<div id="chart">
<slot name="dragHandle"></slot>
<div id="{{plotId}}"></div>
</div>
<paper-dialog id="loadTrack" modal>
<h2 style="text-align:center; color: #4285f4">Add a New Track</h2>
<div class="content">
<form is="iron-form" id="trackSettings">
<paper-input class="fElement" name="name" label="Track Name" value="{{trackSelected.name}}"></paper-input>
<paper-dropdown-input name="type" label="Choose Track Type " items="[[igvTrackTypes]]" value="{{trackSelected.type}}">
<template>
<template id="trackTypesDOM" is="dom-repeat" items="[[items]]" as="item">
<div class="igv-track-type-row" horizontal layout label="[[item.label]]" on-click="_trackTypeSelected">
<div>
<h3>[[item.trackType]] ([[item.fileTypes]])</h3>
<p>[[item.description]]</p>
</div>
</div>
</template>
</template>
</paper-dropdown-input>
<!-- <paper-input name="format" label="File Extension" value="{{trackSelected.format}}"></paper-input> -->
<paper-dropdown-input class="fElement" label="File Type" items="[[igvFileFormats]]" value="{{trackSelected.format}}"></paper-dropdown-input>
<paper-input class="fElement" name="url" label="File location URL" value="{{trackSelected.url}}"></paper-input>
<paper-input class="fElement" name="indexURL" label="indexURL (optional)" value="{{trackSelected.indexURL}}"></paper-input>
<div class="fElement" style="display: block;">
Choose Track Color :
<paper-swatch-picker id="colorPicker" name="color" label="Track Color (optional)" color="{{trackSelected.color}}"></paper-swatch-picker>
</div>
</form>
</div>
<div class="buttons">
<paper-button id="submit" raised>Add Track</paper-button>
<paper-button dialog-dismiss>Close</paper-button>
</div>
</paper-dialog>
</template>
<script>
// Extend Polymer.Element base class
class EpivizIGVTrack extends Polymer.Element {
static get is() { return 'epiviz-igv-track'; }
static get properties() {
return {
reference: {
type: String,
notify: true,
reflectInAttribute: true,
value: function () {
return "hg19";
}
},
showNavigation: {
type: Boolean,
notify: true,
reflectInAttribute: true,
value: function () {
return true;
}
},
showRuler: {
type: Boolean,
notify: true,
reflectInAttribute: true,
value: function () {
return false;
}
},
genome: {
type: String,
notify: true,
reflectInAttribute: true,
value: function () {
return "hg19";
}
},
locus: {
type: String,
notify: true,
reflectInAttribute: true,
computed: "_getLocus(chr, start, end)"
},
tracks: {
type: Array,
notify: true,
value: [],
reflectInAttribute: true
},
trackTypes: {
type: Array,
notify: true,
value: ['annotation', 'wig', 'alignment', 'variant', 'seg']
},
trackSelected: {
type: Object,
notify: true,
value: {}
},
chr: {
type: String,
notify: true,
value: "chr8"
},
start: {
type: Number,
notify: true,
value: 128747267
},
end: {
type: Number,
notify: true,
value: 128754546
},
igvTrackTypes: {
type: Array,
notify: true,
value: function () {
return [
{
"label": "annotation",
"trackType": "annotation", "fileTypes": "bed, gff, gff3, gtf",
"description": "For displaying non-quantitative genome annotations such as genes. This is the most generic track type."
},
{
"label": "wig",
"trackType": "wig", "fileTypes": "wig, bigWig, bedGraph",
"description": "For displaying quantitative genomic data, such as ChIP peaks and alignment coverage."
},
{
"label": "alignment",
"trackType": "alignment", "fileTypes": "bam",
"description": "For displaying read alignments."
},
{
"label": "variant",
"trackType": "variant", "fileTypes": "vcf",
"description": "For displaying genome variants."
},
{
"label": "seg",
"trackType": "seg", "fileTypes": "seg",
"description": "For displaying segmented copy number data."
}
]
}
},
igvFileFormats: {
type: Array,
value: [],
notify: true
}
}
}
static get observers() {
return [
/* observer array just like 1.x */
"_tracksChanged(tracks.*)"
]
}
constructor() {
super();
this.addEventListener('submit.click', e => this._submit(e));
}
/* lifecycle callback function after the element is ready */
connectedCallback() {
super.connectedCallback();
var self = this;
self.plotId = self.plotId || self._generatePlotId();
var parent = self.parentNode;
var tracks = [
{
name: "Genes",
type: "annotation",
format: "bed",
sourceType: "file",
url: "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/refGene.hg19.bed.gz",
indexURL: "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/refGene.hg19.bed.gz.tbi",
order: Number.MAX_VALUE,
visibilityWindow: 300000000,
displayMode: "EXPANDED"
}, {
name: "Phase 3 WGS variants",
format: "vcf",
url: "https://s3.amazonaws.com/1000genomes/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz",
indexURL: "https://s3.amazonaws.com/1000genomes/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi",
type: "variant"
}
];
self.tracks = tracks;
}
disconnectedCallback() {
super.disconnectedCallback();
}
ready() {
super.ready();
var self = this;
this.$.trackSettings.addEventListener('iron-form-submit', this._form_submit.bind(self));
// self.scopeSubtree(self.$.chart, true);
parent.addEventListener('hoverAllCharts', function (e) {
self.chart.hover(e.detail.data);
}.bind(self));
parent.addEventListener('unHoverAllCharts', function (e) {
self.chart.unHover();
}.bind(self));
}
_getLocus(chr, start, end) {
return chr + ":" + start + "-" + end;
}
_trackTypeSelected(e) {
this.push("igvFileFormats", []);
this.igvFileFormats = event.model.get("item.fileTypes").split(",");
this.push("igvFileFormats", event.model.get("item.fileTypes").split(","));
}
_submit(event) {
this.$.trackSettings.submit();
}
/**
* handles form submit action
*/
_form_submit(event) {
var self = this;
this.vals = event.detail;
this.vals.color = self.$.colorPicker.color;
// console.log(this.vals);
self.push("tracks", this.vals);
self.$.loadTrack.close();
}
_addTrack() {
this.set("trackSelected", {})
this.trackSelected = {};
this.$.loadTrack.open();
}
_editTrack(e) {
var track = this.$.dataTracks.itemForElement(e.target);
this.set("trackSelected", track);
this.$.loadTrack.open();
}
/**
* Generates a unique chart ID
*
* @return {string}
*/
_generatePlotId() {
var chars = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ';
var result = '';
var size = 7;
for (var i = 0; i < size; ++i) {
result += chars[Math.round(Math.random() * (chars.length - 1))];
}
return 'epiviz-' + result;
}
/**
* ChartLocation/RangeChange event handler.
*/
_rangeChanged() {
if (this.chromosome != null && this.start != null && this.end != null) {
if (this.plotId) {
this._draw();
}
}
}
_tracksChanged(newTrack, oldTrack) {
this._draw();
}
/**
* Hover event handler.
*
* @param {object} data data object currently hovered.
*/
hover(data) {
var self = this;
if (data.seqName == this.chr) {
var hoverCanvas = self.$.chart.querySelector("canvas.igv-ideogram-canvas");
var canvasWidth = parseInt(hoverCanvas.width);
var canvasHeight = parseInt(hoverCanvas.height)
var width = self.end - self.start;
var ratio = width / canvasWidth;
// this.chart.doHover(data);
this._draw();
setTimeout(function () {
var canvas = self.$.chart.querySelectorAll("canvas");
canvas.forEach(function (cElem) {
var ctx = cElem.getContext("2d");
ctx.beginPath();
ctx.fillStyle = "#ffc600";
ctx.globalAlpha = 0.2;
var x = data.start - self.start;
var w = data.end - self.start;
ctx.rect(
x / ratio,
0,
w / ratio,
canvasHeight
);
ctx.fill();
});
}, 500);
}
}
/**
* unHover event handler.
*/
unHover() {
// this.chart.doUnhover();
this._draw();
}
/**
* Draws the chart.
*/
_draw() {
var self = this;
$(self.shadowRoot.querySelector("#" + self.plotId)).empty();
var div = self.shadowRoot.querySelector("#" + self.plotId);
var options = {
reference: {
id: self.reference,
fastaURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/1kg_v37/human_g1k_v37_decoy.fasta",
cytobandURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/b37/b37_cytoband.txt"
},
locus: self.locus,
tracks: JSON.parse(JSON.stringify(self.tracks))
};
self.browser = igv.createBrowser(div, options);
setTimeout(function () {
var hoverCanvas = self.$.chart.querySelector("canvas.igv-ideogram-canvas");
var canvasWidth = parseInt(hoverCanvas.width);
var width = self.end - self.start;
var ratio = width / canvasWidth;
var canvas = self.$.chart.querySelectorAll("canvas");
canvas.forEach(function (cElem) {
cElem.addEventListener("mousemove", function (event) {
var rect = cElem.getBoundingClientRect();
var x = event.clientX;
var y = event.clientY;
var start = self.start;
var width = ratio * x;
var elem = new epiviz.ui.charts.ChartObject(
sprintf("igv-track", self.plotId),
start + width - 10,
start + width + 10,
undefined, undefined, undefined, undefined, undefined, self.chr
);
self.dispatchEvent(new CustomEvent('hover',
{
detail: {
data: elem
},
bubbles: true
}
));
});
cElem.addEventListener("mouseout", function (event) {
self.dispatchEvent(new CustomEvent('unHover',
{
detail: {
data: null
},
bubbles: true
}
)
);
});
});
}, 500);
}
};
customElements.define(EpivizIGVTrack.is, EpivizIGVTrack);
</script>
</dom-module>