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epiviz-heatmap-plot.html
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epiviz-heatmap-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">
<!-- Epiviz Shared css -->
<link rel="import" type="css" 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-heatmap-plot>` creates a heatmap where columns are aligned to the genomic location.
Element attributes are defined in <a href="#epiviz.ChartBehavior">`<epiviz.ChartBehavior>`</a> element.
To create a heatmap on a HTML page, add
<epiviz-heatmap-plot></epiviz-heatmap-plot>
@demo demo/index-heatmap-plot.html Example page showing a heatmap-plot
-->
<dom-module id="epiviz-heatmap-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>
<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 EpivizHeatmapPlot extends EpivizChartGridBehavior(EpivizChartRemoveBehavior(EpivizChartColorsBehavior(EpivizChartSettingsBehavior(EpivizChartBehavior(Polymer.Element))))) {
static get is() { return 'epiviz-heatmap-plot'; }
static get properties() {
return {
/**
* Default chart properties for heatmap plot.
*
* @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: '100%',
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.HeatmapPlot': {
width: 800,
height: 400,
margins: new epiviz.ui.charts.Margins(80, 120, 40, 40),
decorations: [
'epiviz.ui.charts.decoration.ChartGroupByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartOrderByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartColorByRowCodeButton'
],
colors: 'heatmap-default'
}
},
chartCustomSettings: {
'epiviz.plugins.charts.HeatmapPlot': {
colLabel: 'label',
maxColumns: 120,
clusteringAlg: 'agglomerative'
}
},
clustering: {
algorithms: [
'epiviz.ui.charts.transform.clustering.NoneClustering',
'epiviz.ui.charts.transform.clustering.AgglomerativeClustering'
],
metrics: ['epiviz.ui.charts.transform.clustering.EuclideanMetric'],
linkages: ['epiviz.ui.charts.transform.clustering.CompleteLinkage']
},
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();
}
disconnectedCallback() {
super.connectedCallback();
}
ready() {
super.ready();
this.plotId = self.plotId || this._generatePlotId();
// this.scopeSubtree(this.$.chart, true);
this.config = new epiviz.Config(this.configSrc);
epiviz.ui.charts.transform.clustering.ClusteringAlgorithmFactory.initialize(this.config);
}
/**
* Draws the chart.
*
* @param {Object<epiviz.datatypes.GenomicRange>} range genomic range.
* @param {Object<epiviz.datatypes.MapGenomicData>} data to plot
*/
_draw() {
if(this.data && this.data.measurements().length == this.measurements.length) {
if (this.canvas) {
this.chart.drawCanvas(this.range, this.data);
}
else {
this.chart.draw(this.range, this.data);
}
this.shadowRoot.querySelector("paper-spinner-lite").active = false;
}
}
/**
* Creates an instance of the Heatmap plot chart.
*
* @return {epiviz.plugins.charts.HeatmapPlotType} HeatmapPlot chart object
*/
_createChart() {
var self = this;
return new epiviz.plugins.charts.HeatmapPlotType(new epiviz.Config(this.configSrc));
}
};
customElements.define(EpivizHeatmapPlot.is, EpivizHeatmapPlot);
</script>
</dom-module>