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epiviz-line-track-mirror.html
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epiviz-line-track-mirror.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-log-ratio.html">
<link rel="import" href="chart-negation.html">
<link rel="import" href="chart-average.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-line-track-mirror>` visualizes various measurements on the same track with x-axis as genomic region
Element attributes are defined in <a href="#epiviz.ChartBehavior">`<epiviz.ChartBehavior>`</a> element.
To create a line track on a HTML page, add
<epiviz-line-track-mirror></epiviz-line-track-mirror>
@demo demo/index-line-track.html Example page showing a line track
-->
<dom-module id="epiviz-line-track-mirror">
<!--<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 EpivizLineTrackMirror extends EpivizChartGridBehavior(
EpivizChartAverageBehavior(
EpivizChartNegationBehavior(
EpivizChartLogRatioBehavior(
EpivizChartRemoveBehavior(
EpivizChartColorsBehavior(
EpivizChartSettingsBehavior(
EpivizChartBehavior(
Polymer.Element)))))))) {
static get is() { return 'epiviz-line-track-mirror'; }
static get properties() {
return {
/**
* Default chart properties for 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.LineTrack': {
colors: 'epiviz-v2-bright',
decorations: [
'epiviz.ui.charts.decoration.ChartGroupByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartColorByMeasurementsCodeButton'
]
},
},
chartCustomSettings: {
'epiviz.plugins.charts.LineTrack': {
step: 1,
showPoints: false,
showLines: true,
pointRadius: 1,
lineThickness: 2
},
},
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;
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);
}
/**
* Draws the chart.
*
* @param {Object<epiviz.datatypes.GenomicRange>} range genomic range.
* @param {Object<epiviz.datatypes.MapGenomicData>} data to plot
*/
_draw() {
var self = this;
if(this.data) {
if (self.invertcell) {
var data = this.get_invert_data_mirror1(this.data, this.invertcell);
}
else {
var data = this.get_invert_data(this.data);
}
this.isNegation = true;
if (this.canvas) {
this.chart.drawCanvas(this.range, this.data);
}
else {
this.chart.draw(this.range, data, undefined, undefined, self.isNegation);
}
if (this.data.measurements().length == this.measurements.length) {
this.shadowRoot.querySelector("paper-spinner-lite").active = false;
}
}
}
get_invert_data_mirror1(lData, celltype) {
var self = this;
var sumExp = new epiviz.datatypes.PartialSummarizedExperiment();
var counter = 0;
// var invert = 0;
lData.foreach(function(measurement, series, seriesIndex) {
if(counter == 0) {
var rowData = series._container.rowData(measurement);
sumExp._rowData = rowData;
counter++;
}
var featureValues = series._container.values(measurement);
var valData = [];
if(featureValues._values != undefined) {
if(measurement.id().indexOf(celltype) == -1) {
featureValues._values.forEach(function(val, i) {
valData[i] = -1 * val;
});
}
else {
featureValues._values.forEach(function(val, i) {
valData[i] = val;
});
}
// invert++;
}
else {
valData = undefined;
}
var newValueData = new epiviz.datatypes.FeatureValueArray(measurement, featureValues._boundaries, featureValues._globalStartIndex, valData);
sumExp.addValues(newValueData);
// invert++;
});
var msDataMap = new epiviz.measurements.MeasurementHashtable();
lData.foreach(function(m) {
m._maxValue = m._maxValue;
m._minValue = -1 * m._maxValue;
var msData = new epiviz.datatypes.MeasurementGenomicDataWrapper(m, sumExp);
msDataMap.put(m, msData);
});
var genomicData = new epiviz.datatypes.MapGenomicData(msDataMap);
return genomicData
}
get_invert_data(lData) {
var self = this;
var sumExp = new epiviz.datatypes.PartialSummarizedExperiment();
var counter = 0;
// var invert = 0;
lData.foreach(function(measurement, series, seriesIndex) {
if(counter == 0) {
var rowData = series._container.rowData(measurement);
sumExp._rowData = rowData;
counter++;
}
var featureValues = series._container.values(measurement);
var valData = [];
if(featureValues._values != undefined) {
// if (measurement.name().indexOf("Lamp5") != -1 || measurement.name().indexOf("Sst") != -1 ||
// measurement.name().indexOf("Vip") != -1 || measurement.name().indexOf("Pvalb") != -1) {
if( (measurement.name().indexOf("Lamp5") != -1 || measurement.name().indexOf("Sst") != -1 ||
measurement.name().indexOf("Vip") != -1 || measurement.name().indexOf("Pvalb") != -1) || (measurement.id().indexOf("gaba") != -1)) {
featureValues._values.forEach(function(val, i) {
valData[i] = -1 * val;
});
}
else {
featureValues._values.forEach(function(val, i) {
valData[i] = val;
});
}
}
else {
valData = undefined;
}
var newValueData = new epiviz.datatypes.FeatureValueArray(measurement, featureValues._boundaries, featureValues._globalStartIndex, valData);
sumExp.addValues(newValueData);
// invert++;
});
var msDataMap = new epiviz.measurements.MeasurementHashtable();
lData.foreach(function(m) {
m._maxValue = m._maxValue;
m._minValue = -1 * m._maxValue;
var msData = new epiviz.datatypes.MeasurementGenomicDataWrapper(m, sumExp);
msDataMap.put(m, msData);
});
var genomicData = new epiviz.datatypes.MapGenomicData(msDataMap);
return genomicData
}
/**
* Creates an instance of the line track chart.
*
* @return {epiviz.plugins.charts.LineTrackType} LineTrack chart object
*/
_createChart() {
return new epiviz.plugins.charts.LineTrackType(new epiviz.Config(this.configSrc));
}
};
customElements.define(EpivizLineTrackMirror.is, EpivizLineTrackMirror);
// Polymer({
// /* Custom element html tag */
// is: 'epiviz-line-track-mirror',
// behaviors: [epiviz.ChartBehavior, epiviz.ChartSettingsBehavior, epiviz.ChartColorsBehavior, epiviz.ChartRemoveBehavior, Polymer.IronResizableBehavior, epiviz.ChartDraggableBehavior],
// });
</script>
</dom-module>