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epiviz-sashimi-plot.html
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epiviz-sashimi-plot.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"> -->
<!-- Epiviz Polymer Behaviors dependency -->
<link rel="import" href="chart-behavior.html" />
<link rel="import" href="chart-settings.html" />
<link rel="import" href="chart-colors.html" />
<link rel="import" href="chart-remove.html" />
<link rel="import" href="chart-grid-behavior.html" />
<link rel="import" href="chart-showtracks.html" />
<link rel="import" href="chart-fixed-axis-toggle.html" />
<!-- Epiviz Shared css -->
<link rel="import" href="chart-shared-css.html" />
<!--
<h2> Chart Component </h2>
epiviz-chart components are a collection of reusable and extensible visualization components for
genomic data.
An epiviz-chart component requires two attributes to render a visualization on the page
<ul>
<li>data attribute, </li>
<li>dimensions (or columns) from the data attribute to visualize.</li>
</ul>
`<epiviz-sashimi-plot>` is similar to line track with genomic location on the x-axis
and can be used to visualize multiple annotation regions on the same track.
Element attributes are defined in <a href="#epiviz.ChartBehavior">`<epiviz.ChartBehavior>`</a> element.
To create a stacked-blocks plot on a HTML page, add
<epiviz-sashimi-plot></epiviz-sashimi-plot>
@demo demo/index-stacked-line-track.html Example page showing a stacked-line track
-->
<dom-module id="epiviz-sashimi-plot">
<!--<link rel="import" href="bower_components/epiviz-imports/epiviz-common-css.html">-->
<template>
<style include="shared-settings"></style>
<style include="chart-shared-css"></style>
<link
rel="stylesheet"
href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css"
/>
<style>
:host {
width: 100%;
height: 100%;
display: inline-block;
border: 1px solid black;
border-radius: 5px;
resize: vertical;
overflow: auto;
transition: width 0.01s, height 0.01s;
position: relative;
}
</style>
<!-- local DOM goes here -->
<paper-spinner-lite active class="green"></paper-spinner-lite>
<div id="chart" on-mouseover="hostHovered" on-mouseout="hostUnhovered">
<slot name="dragHandle"></slot>
<div id="{{plotId}}"></div>
</div>
</template>
<script>
// Extend Polymer.Element base class
class EpivizSashimiPlot extends EpivizFixedAxisBehavior(
EpivizChartShowTracksBehavior(
EpivizChartGridBehavior(
EpivizChartRemoveBehavior(
EpivizChartColorsBehavior(
EpivizChartSettingsBehavior(EpivizChartBehavior(Polymer.Element))
)
)
)
)
) {
static get is() {
return "epiviz-sashimi-plot";
}
static get properties() {
return {
/**
* Default chart properties for stacked-line track.
*
* @type {Object}
*/
configSrc: {
type: Object,
notify: true,
value: function () {
epiviz.Config.SETTINGS = {
dataProviders: [
[
"epiviz.data.WebServerDataProvider",
"umd",
"http://epiviz-dev.cbcb.umd.edu/api/",
],
],
workspacesDataProvider: sprintf(
"epiviz.data.EmptyResponseDataProvider",
"empty",
""
),
useCache: true,
chartSettings: {
default: {
colors: "d3-category10",
decorations: [
"epiviz.ui.charts.decoration.RemoveChartButton",
"epiviz.ui.charts.decoration.SaveChartButton",
"epiviz.ui.charts.decoration.CustomSettingsButton",
"epiviz.ui.charts.decoration.EditCodeButton",
"epiviz.ui.charts.decoration.ChartColorsButton",
"epiviz.ui.charts.decoration.ChartLoaderAnimation",
"epiviz.ui.charts.decoration.ChartResize",
],
},
plot: {
width: 400,
height: 400,
margins: new epiviz.ui.charts.Margins(15, 30, 30, 15),
decorations: [
"epiviz.ui.charts.decoration.ToggleTooltipButton",
"epiviz.ui.charts.decoration.ChartTooltip",
"epiviz.ui.charts.decoration.ChartFilterCodeButton",
],
},
track: {
width: 900,
height: 90,
margins: new epiviz.ui.charts.Margins(25, 40, 23, 10),
decorations: [
"epiviz.ui.charts.decoration.ToggleTooltipButton",
"epiviz.ui.charts.decoration.ChartTooltip",
"epiviz.ui.charts.decoration.ChartFilterCodeButton",
],
},
"epiviz.plugins.charts.SashimiPlot": {
height: 300,
},
},
chartCustomSettings: {
"epiviz.plugins.charts.SashimiPlotType": {
// step: 1,
showPoints: false,
// showLines: true,
pointRadius: 1,
// lineThickness: 2,
interpolation: "basis",
},
},
colorPalettes: [
new epiviz.ui.charts.ColorPalette(
[
"#025167",
"#e7003e",
"#ffcd00",
"#057d9f",
"#970026",
"#ffe373",
"#ff8100",
],
"Epiviz v1.0 Colors",
"epiviz-v1"
),
new epiviz.ui.charts.ColorPalette(
[
"#1859a9",
"#ed2d2e",
"#008c47",
"#010101",
"#f37d22",
"#662c91",
"#a11d20",
"#b33893",
],
"Epiviz v2.0 Bright",
"epiviz-v2-bright"
),
new epiviz.ui.charts.ColorPalette(
[
"#b8d2eb",
"#f2aeac",
"#d8e4aa",
"#cccccc",
"#f2d1b0",
"#d4b2d3",
"#ddb8a9",
"#ebbfd9",
],
"Epiviz v2.0 Light",
"epiviz-v2-light"
),
new epiviz.ui.charts.ColorPalette(
[
"#599ad3",
"#f1595f",
"#79c36a",
"#727272",
"#f9a65a",
"#9e66ab",
"#cd7058",
"#d77fb3",
],
"Epiviz v2.0 Medium",
"epiviz-v2-medium"
),
new epiviz.ui.charts.ColorPalette(
[
"#1f77b4",
"#ff7f0e",
"#2ca02c",
"#d62728",
"#9467bd",
"#8c564b",
"#e377c2",
"#7f7f7f",
"#bcbd22",
"#17becf",
],
"D3 Category 10",
"d3-category10"
),
new epiviz.ui.charts.ColorPalette(
[
"#1f77b4",
"#aec7e8",
"#ff7f0e",
"#ffbb78",
"#2ca02c",
"#98df8a",
"#d62728",
"#ff9896",
"#9467bd",
"#c5b0d5",
"#8c564b",
"#c49c94",
"#e377c2",
"#f7b6d2",
"#7f7f7f",
"#c7c7c7",
"#bcbd22",
"#dbdb8d",
"#17becf",
"#9edae5",
],
"D3 Category 20",
"d3-category20"
),
new epiviz.ui.charts.ColorPalette(
[
"#393b79",
"#5254a3",
"#6b6ecf",
"#9c9ede",
"#637939",
"#8ca252",
"#b5cf6b",
"#cedb9c",
"#8c6d31",
"#bd9e39",
"#e7ba52",
"#e7cb94",
"#843c39",
"#ad494a",
"#d6616b",
"#e7969c",
"#7b4173",
"#a55194",
"#ce6dbd",
"#de9ed6",
],
"D3 Category 20b",
"d3-category20b"
),
new epiviz.ui.charts.ColorPalette(
[
"#3182bd",
"#6baed6",
"#9ecae1",
"#c6dbef",
"#e6550d",
"#fd8d3c",
"#fdae6b",
"#fdd0a2",
"#31a354",
"#74c476",
"#a1d99b",
"#c7e9c0",
"#756bb1",
"#9e9ac8",
"#bcbddc",
"#dadaeb",
"#636363",
"#969696",
"#bdbdbd",
"#d9d9d9",
],
"D3 Category 20c",
"d3-category20c"
),
new epiviz.ui.charts.ColorPalette(
[
"#f9a65a",
"#599ad3",
"#79c36a",
"#f1595f",
"#727272",
"#cd7058",
"#d77fb3",
],
"Genes Default",
"genes-default"
),
new epiviz.ui.charts.ColorPalette(
[
"#1859a9",
"#ed2d2e",
"#008c47",
"#010101",
"#f37d22",
"#662c91",
"#a11d20",
"#b33893",
],
"Heatmap Default",
"heatmap-default"
),
],
};
return epiviz.Config.SETTINGS;
},
},
};
}
static get observers() {
return [
/* observer array just like 1.x */
];
}
constructor() {
super();
}
connectedCallback() {
super.connectedCallback();
var self = this;
if (self.useDefaultDataProvider) {
self.measurements = self.measurements || [
{
id: "e027",
name: "Expression Colon Cancer",
type: "feature",
datasourceId: "roadmap_rnaseq",
datasourceGroup: "roadmap_rnaseq",
dataprovider: "umd",
formula: null,
defaultChartType: null,
annotation: null,
minValue: -3,
maxValue: 20,
metadata: ["probe"],
},
{
id: "e066",
name: "Expression Colon Normal",
type: "feature",
datasourceId: "roadmap_rnaseq",
datasourceGroup: "roadmap_rnaseq",
dataprovider: "umd",
formula: null,
defaultChartType: null,
annotation: null,
minValue: -3,
maxValue: 20,
metadata: ["probe"],
},
];
self.range =
self.range ||
new epiviz.datatypes.GenomicRange("chr11", 80000000, 3000000);
// self._measurementsChanged();
var chartMeasMap = {};
chartMeasMap[self.plotId] = self.visConfigSelection.measurements;
var dataProviderFactory = new epiviz.data.DataProviderFactory(
self.config
);
var dataManager = new epiviz.data.DataManager(
self.config,
dataProviderFactory
);
dataManager.getData(self.range, chartMeasMap, function (id, data) {
self.data = data;
});
}
self._initializeGrid();
self._measurementsChanged();
if (self.dimS) {
this.style =
"min-height:" + Math.max(200, self.dimS.length * 125) + "px;";
} else if (self.measurements) {
this.style =
"min-height:" +
Math.max(200, self.measurements.length * 125) +
"px;";
} else {
this.style = "min-height:" + 250 + "px;";
}
}
disconnectedCallback() {
super.connectedCallback();
}
ready() {
super.ready();
this.plotId = self.plotId || this._generatePlotId();
// this.scopeSubtree(this.$.chart, true);
this.config = new epiviz.Config(this.configSrc);
}
/**
* Draws the chart.
*
* @param {Object<epiviz.datatypes.GenomicRange>} range genomic range.
* @param {Object<epiviz.datatypes.MapGenomicData>} data to plot
*/
_draw() {
if (this.data) {
// if (this.canvas) {
// this.chart.drawCanvas(this.range, this.data);
// } else {
// this.chart.draw(this.range, this.data);
// }
this.chart.draw(this.range, this.data);
if (this.data.measurements().length == this.measurements.length) {
this.shadowRoot.querySelector("paper-spinner-lite").active = false;
}
}
}
/**
* Creates an instance of the stacked-line track chart.
*
* @return {epiviz.plugins.charts.StackedLineTrackType} StackedLineTrack chart object
*/
_createChart() {
return new epiviz.plugins.charts.SashimiPlotType(
new epiviz.Config(this.configSrc)
);
}
}
customElements.define(EpivizSashimiPlot.is, EpivizSashimiPlot);
// Polymer({
// /* Custom element html tag */
// is: 'epiviz-sashimi-plot',
// behaviors: [epiviz.ChartBehavior, epiviz.ChartSettingsBehavior, epiviz.ChartColorsBehavior, epiviz.ChartRemoveBehavior, Polymer.IronResizableBehavior, epiviz.ChartDraggableBehavior],
// });
</script>
</dom-module>