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chart-json-behavior.html
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chart-json-behavior.html
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<!-- External Polymer Styles/elements dependency -->
<link rel="import" href="bower_components/iron-resizable-behavior/iron-resizable-behavior.html">
<script>
/**
* `ChartJSONBehavior` is an interface to all epiviz-json-charts.
* This behavior provides functionality to convert json-data into a `epiviz.datatypes.MapGenomicData` format.
*
* @polymerBehavior
**/
EpivizJSONChartBehavior = function (superClass) {
return class extends superClass {
constructor() {
super();
this.addEventListener('keypress', e => this.handlePress(e));
}
static get properties() {
return {
/**
* json data object.
*
* @type {Object} data
* @property {Array<Object>} data.cols For each column, array of values.
* @property {Array<Object>} data.rows For each row metadata, array of values.
* @property {Array<Object>} data.colAnnotation For each column, annotations if available
*/
data: {
type: Object,
notify: true
// observer: '_dataChanged'
},
/**
* Dimensions for a chart from data object. (x and y axis measurements).
*
* @type {Array<string>}
*/
dimS: {
type: Array,
notify: true
// observer: '_dimsChanged'
},
/**
* Measurements for a chart from data Object.
*
* @type {Array<string>}
*/
measurements: {
type: Array,
notify: true
},
/**
* json data key to use for hovering.
*
* @type {string}
*/
key: {
type: Array,
notify: true
},
/**
* Chart json data object.
*
* @type {Object}
*/
_chartData: {
type: Object,
notify: true
},
/**
* Chromosome location.
* Default Location Attribute to set to all the children chart elements.
*
* @example: chr1
*
* @type {string}
*/
chr: {
type: String,
notify: true
},
/**
* Chromosome start.
* Default Chromosome start value to use. (defaults to 0).
*
* @type {number}
*/
start: {
type: Number,
notify: true
},
/**
* Chromosome end.
* Default Chromosome end value to use. (defaults to the `<chr>` length).
*
* @type {number}
*/
end: {
type: Number,
notify: true
},
/**
* Chart range.
*
* @type {Object<epiviz.datatypes.GenomicRange>}
*/
range: {
type: Object,
notify: true,
computed: 'getGenomicRange(chr, start, end)',
},
/**
* Chart json measurements object.
*
* @type {Object}
*/
_chartMeasurements: {
type: Array,
notify: true
},
/**
* Chart setings.
*
* @type {Object}
*/
settings: {
type: Object,
notify: true
},
/**
* Chart colors.
*
* @type {Object}
*/
colors: {
type: Array,
notify: true
}
};
}
static get observers() {
return ['_barChanged(bar.*)'];
}
ready() {
super.ready();
var self = this;
self.plotId = this.$.epivizChart.plotId;
var m = [];
var mSet = new epiviz.measurements.MeasurementSet();
var datasource = "epiviz";
var rowLength = 0;
var hasfData = true;
var measurementType = 'feature';
var useOffset = false;
if (self.nodeName === "EPIVIZ-JSON-GENES-TRACK") {
measurementType = 'range';
}
if (Object.keys(self.data).indexOf("format") != -1 && self.data.format == "epiviz") {
if (self.measurements) {
self.measurements.forEach(function (mea) {
mSet.add(new epiviz.measurements.Measurement(
mea.id, mea.name, mea.type, mea.datasourceId, mea.datasourceGroup, mea.dataprovider,
mea.formula, mea.defaultChartType, mea.annotation, mea.minValue, mea.maxValue, mea.metadata
));
});
m = self.measurements;
}
else if (self.dimS) {
self.dimS.forEach(function (dim) {
var colValues = [0, 5];
if (self.data.cols) {
colValues = self.data.cols[dim] || self.data.cols[dim].values;
}
// var colValues = self.data.cols[dim];
var rowLength = colValues.length;
m.push({
'id': dim,
'name': dim,
'type': measurementType,
'datasourceId': datasource,
'datasourceGroup': dim,
'dataprovider': datasource,
'formula': null,
'defaultChartType': self.chartName,
'annotation': undefined,
'minValue': Math.min.apply(Math, colValues),
'maxValue': Math.max.apply(Math, colValues),
'metadata': rowMetadata
});
if (!hasfData) {
self.data.cols[dim] = { "values": [] }
}
mSet.add(new epiviz.measurements.Measurement(
dim, dim, measurementType, datasource, dim, datasource, null, self.chartName, undefined, null, null, rowMetadata
));
});
}
self._chartMeasurements = m;
var chartData = new epiviz.measurements.MeasurementHashtable();
mSet.foreach(function (m) {
var mData = self.data[m.datasourceId()];
var rowLength = mData.rows.values.chr.length;
if (!self.chr) {
self.chr = mData.rows.values.chr[0];
}
if (!self.start) {
self.start = mData.rows.values.start[0];
}
if (!self.end) {
self.end = mData.rows.values.end[rowLength - 1];
}
if (!self.range) {
self.range = new epiviz.datatypes.GenomicRange(mData.rows.values.chr[0], mData.rows.values.start[0], mData.rows.values.end[rowLength - 1] - mData.rows.values.start[0]);
}
var sumExp = new epiviz.datatypes.PartialSummarizedExperiment();
var rowDataObj = new epiviz.datatypes.GenomicRangeArray(m, self.range, mData.rows.globalStartIndex, mData.rows.values, mData.rows.useOffset);
sumExp.addRowData(rowDataObj);
if (mData.cols) {
var valueData = new epiviz.datatypes.FeatureValueArray(m, self.range, mData.cols[m.id()].globalStartIndex, mData.cols[m.id()].values);
sumExp.addValues(valueData);
}
var msData = new epiviz.datatypes.MeasurementGenomicDataWrapper(m, sumExp);
chartData.put(m, msData);
self._chartRange = self.range;
});
var genomicData = new epiviz.datatypes.MapGenomicData(chartData);
self._chartData = genomicData;
}
else if (Object.keys(self.data).indexOf("format") != -1 && self.data.format == "epivizMultiRegion") {
if (!self.measurements) {
var regions = Object.keys(self.data);
var rowLength = 0;
regions.splice(regions.indexOf("format"), 1);
regions.forEach(function (reg) {
var keysRegs = Object.keys(self.data[reg].cols.values);
keysRegs.forEach(function (k) {
m.push({
'id': k,
'name': k,
'type': measurementType,
'datasourceId': reg,
'datasourceGroup': reg,
'dataprovider': datasource,
'formula': null,
'defaultChartType': self.chartName,
'annotation': { "tissue": "colon", "tumorType": "normal" },
'minValue': 0,
'maxValue': 1,
'metadata': ["chr", "start", "end"]
});
mSet.add(new epiviz.measurements.Measurement(
k, k, measurementType, reg, reg, datasource, null, self.chartName, { "tissue": "colon", "tumorType": "normal" }, null, null, []
));
});
rowLength = self.data[reg].rows.values.chr.length;
});
}
else {
m = self.measurements;
m.forEach(function (tm) {
mSet.add(new epiviz.measurements.Measurement(
tm.id, tm.name, tm.type, tm.datasourceId,
tm.datasourceGroup, tm.dataprovider, tm.formula, tm.defaultChartType,
tm.annotation, tm.minValue, tm.maxValue, tm.metadata
));
rowLength = self.data[tm.datasourceId].rows.values.chr.length;
});
}
self._chartMeasurements = m;
var chartData = new epiviz.measurements.MeasurementHashtable();
self.chr = "epivizMultiRegion"
self.start = 1;
self.end = rowLength;
var rowObj = self._generateRowIndexes(rowLength);
mSet.foreach(function (m) {
var mData = self.data[m.datasourceId()];
rowObj.metadata = mData.rows.values;
delete rowObj.metadata["metadata"];
delete rowObj.metadata["id"];
delete rowObj.metadata["strand"];
delete rowObj.metadata["id"];
var sumExp = new epiviz.datatypes.PartialSummarizedExperiment();
var rowDataObj = new epiviz.datatypes.GenomicRangeArray(m, self.range, 1, rowObj, false);
sumExp.addRowData(rowDataObj);
if (mData.cols) {
var valueData = new epiviz.datatypes.FeatureValueArray(m, self.range, 1, mData.cols.values[m.id()]);
sumExp.addValues(valueData);
}
var msData = new epiviz.datatypes.MeasurementGenomicDataWrapper(m, sumExp);
chartData.put(m, msData);
});
var groupByMarker = new epiviz.ui.charts.markers.VisualizationMarker(
epiviz.ui.charts.markers.VisualizationMarker.Type.GROUP_BY_MEASUREMENTS,
null, null, 'function(a) { return null;}',
'function(a, b, c) {return a.annotation().tumorType;}');
self._chartRange = self.range;
var genomicData = new epiviz.datatypes.MapGenomicData(chartData);
// self._chartData = genomicData;
var groupByMarker = new epiviz.ui.charts.markers.VisualizationMarker(
epiviz.ui.charts.markers.VisualizationMarker.Type.GROUP_BY_MEASUREMENTS,
null, null, 'function(a) { return null;}',
'function(a, b, c) {return a.annotation().tumorType;}');
var aggregator = epiviz.ui.charts.markers.MeasurementAggregators["mean-stdev"];
self.$.epivizChart.chartSettings["showPoints"] = true;
// self.$.epivizChart.chart._lastData = genomicData;
// self.$.epivizChart.chart._markers[groupByMarker.id()] = groupByMarker;
self.aggGenomicData = new epiviz.datatypes.MeasurementAggregatedGenomicData(genomicData, groupByMarker, aggregator);
self.aggGenomicData.ready(function () {
// console.log(self);
self._chartData = self.aggGenomicData;
})
// self.$.epivizChart.chart.transformData(self.range, genomicData).done(function() {
// self._chartData = self.$.epivizChart.chart._lastData;
// });
self.$.epivizChart.addEventListener('hover', function (e) {
if (self.data.format == "epivizMultiRegion") {
e.stopPropagation();
var index = Math.round(e.detail.data.start);
dregions = [];
for (reg in self.data) {
if (reg != "format") {
var region = self.data[reg];
dregions.push(new epiviz.ui.charts.ChartObject(
self.plotId,
region.rows.values.start[index],
region.rows.values.end[index],
undefined, undefined, undefined, undefined, undefined,
region.rows.values.chr[index]));
}
}
self.fire('hover', {
id: self.plotId,
data: dregions
});
}
}.bind(self));
// self.$.epivizChart.addEventListener('select', function(e) {
// if(self.data.format == "epivizMultiRegion") {
// e.stopPropagation();
// var index = Math.round(e.detail.data.start);
// dregions = [];
// for (reg in self.data) {
// if(reg != "format") {
// var region = self.data[reg];
// dregions.push(new epiviz.ui.charts.ChartObject(
// self.plotId,
// region.rows.values.start[index],
// region.rows.values.end[index],
// undefined, undefined, undefined, undefined, undefined,
// region.rows.values.chr[index],));
// }
// }
// self.fire('select', {
// id: self.plotId,
// data: dregions
// });
// }
// }.bind(self));
// self.$.epivizChart.chart.putMarker(groupByMarker);
// self.$.epivizChart.chart.transformData(self.range, genomicData).done(function() {
// self._chartData = self.$.epivizChart.chart._lastData;
// });
}
else {
// if data format is a Array of JSON Objects (long format)
if (Array.isArray(self.data)) {
if (self.key && self.key.length > 0) {
self.data.forEach(function (d) {
var keyFields = [];
self.key.forEach(function (k) {
keyFields.push(d[k]);
});
d.key = keyFields.join("-");
});
}
var rowKeys = Object.keys(self.data[0]);
var colAnnotation = null;
var colsCollection = {}, cols = {};
var rowLength = self.data.length;
rowKeys.forEach(function (key) {
colsCollection[key] = self.data.map(function (r) { return r[key]; });
});
var rowMetadata = rowKeys.slice(0);
var rows = Object.assign({}, colsCollection);
self.dimS.forEach(function (dim) {
var index = rowMetadata.indexOf(dim);
rowMetadata.splice(index, 1);
delete rows[dim];
cols[dim] = colsCollection[dim];
});
self.dimS.forEach(function (dim) {
var colValues = cols[dim];
m.push({
'id': dim,
'name': dim,
'type': measurementType,
'datasourceId': datasource,
'datasourceGroup': dim,
'dataprovider': datasource,
'formula': null,
'defaultChartType': self.chartName,
'annotation': colAnnotation,
'minValue': Math.min.apply(Math, colValues),
'maxValue': Math.max.apply(Math, colValues),
'metadata': rowMetadata
});
mSet.add(new epiviz.measurements.Measurement(
dim, dim, measurementType, datasource, dim, datasource, null, self.chartName, colAnnotation, null, null, rowMetadata
));
});
self._chartMeasurements = m;
/**
* Must have fields
* jsondata.cols
* jsondata.rows
* jsondata.rows.metadata (label)
*/
var jsonData = {};
jsonData.cols = cols;
jsonData.globalStartIndex = 1;
var rowObj = self._generateRowIndexes(rowLength);
rowObj.metadata = rows;
jsonData.rows = rowObj;
}
else {
//if data format is more like a dataframe/data table representation
var rowMetadata = Object.keys(self.data.rows);
var rowLength = 0;
useOffset = self.data.rows.useOffset;
if (self.data.cols == null) { hasfData = false; self.data.cols = {}; }
if (self.data.cols && Object.keys(self.data.cols) > 0) {
if (Object.keys(self.data.cols[Object.keys(self.data.cols)[0]]).indexOf("values") != -1) {
rowLength = self.data.cols[Object.keys(self.data.cols)[0]].values.length;
}
else {
rowLength = self.data.cols[Object.keys(self.data.cols)[0]].length;
}
}
else if (self.data.rows) {
if (Object.keys(self.data.rows).indexOf("values") != -1) {
rowLength = self.data.rows.values[Object.keys(self.data.rows.values)[0]].length;
}
else {
rowLength = self.data.rows[Object.keys(self.data.rows)[0]].length;
}
};
if (self.key && self.key.length > 0) {
var keyArray = [];
for (var ikey = 0; ikey < rowLength; ikey++) {
var keyFields = [];
self.key.forEach(function (k) {
keyFields.push(self.data.rows[k][ikey]);
});
keyArray.push(keyFields.join("-"));
}
self.data.rows.key = keyArray;
}
if (self.measurements) {
self.measurements.forEach(function (mea) {
mSet.add(new epiviz.measurements.Measurement(
mea.id, mea.name, mea.type, mea.datasourceId, mea.datasourceGroup, mea.dataprovider,
mea.formula, mea.defaultChartType, mea.annotation, mea.minValue, mea.maxValue, mea.metadata
));
});
m = self.measurements;
}
else if (self.dimS) {
self.dimS.forEach(function (dim) {
var colValues = [0, 5];
if (self.data.cols) {
colValues = self.data.cols[dim] || self.data.cols[dim].values;
}
// var colValues = self.data.cols[dim];
var rowLength = colValues.length;
m.push({
'id': dim,
'name': dim,
'type': measurementType,
'datasourceId': datasource,
'datasourceGroup': dim,
'dataprovider': datasource,
'formula': null,
'defaultChartType': self.chartName,
'annotation': undefined,
'minValue': Math.min.apply(Math, colValues),
'maxValue': Math.max.apply(Math, colValues),
'metadata': rowMetadata
});
if (!hasfData) {
self.data.cols[dim] = { "values": [] }
}
mSet.add(new epiviz.measurements.Measurement(
dim, dim, measurementType, datasource, dim, datasource, null, self.chartName, undefined, null, null, rowMetadata
));
});
}
self._chartMeasurements = m;
var jsonData = {};
jsonData.cols = {};
if (self.data.cols) {
var colKeys = Object.keys(self.data.cols);
colKeys.forEach(function (ck) {
if (Array.isArray(self.data.cols[ck])) {
jsonData.cols[ck] = self.data.cols[ck];
}
else {
jsonData.cols[ck] = self.data.cols[ck]["values"];
}
});
}
var rowObj = {};
var rowKeys = Object.keys(self.data.rows);
if (rowKeys.indexOf("values") != -1) {
rowObj = self.data.rows.values;
}
else if ((rowKeys.indexOf("start") == -1) || (rowKeys.indexOf("index") == -1) || (rowKeys.rows.indexOf("end") == -1)) {
rowObj = self._generateRowIndexes(rowLength);
rowObj.metadata = self.data.rows;
}
else {
rowObj = self.data.rows;
}
jsonData.globalStartIndex = rowObj.start[0];
jsonData.rows = rowObj;
}
var chartData = new epiviz.measurements.MeasurementHashtable();
var sumExp = new epiviz.datatypes.PartialSummarizedExperiment();
var globalStartIndex = jsonData.globalStartIndex;
var chr = datasource;
if (jsonData.rows.chr) {
chr = jsonData.rows.chr[0];
}
var range = new epiviz.datatypes.GenomicRange(chr, globalStartIndex, jsonData.rows.end[rowLength - 1] - globalStartIndex);
self._chartRange = range;
var rowDataObj = new epiviz.datatypes.GenomicRangeArray(chr, range, globalStartIndex, jsonData.rows, useOffset);
sumExp.addRowData(rowDataObj);
if (hasfData) {
mSet.foreach(function (m) {
var valueData = new epiviz.datatypes.FeatureValueArray(m, range, globalStartIndex, jsonData.cols[m.id()]);
sumExp.addValues(valueData);
});
}
mSet.foreach(function (m) {
var msData = new epiviz.datatypes.MeasurementGenomicDataWrapper(m, sumExp);
chartData.put(m, msData);
});
var genomicData = new epiviz.datatypes.MapGenomicData(chartData);
self._chartData = genomicData;
}
}
getGenomicRange(chr, start, end) {
if (chr && start && end) {
return new epiviz.datatypes.GenomicRange(chr, start, end - start);
}
else {
return null;
}
}
/**
* Helper function to create row-indexes for data items.
*/
_generateRowIndexes(length) {
var rowObj = {};
rowObj.start = [];
rowObj.index = [];
rowObj.id = null;
rowObj.strand = null;
rowObj.chr = [];
rowObj.end = [];
for (var i = 0; i < length; i++) {
rowObj.start.push(i + 1);
rowObj.index.push(i + 1);
// rowObj.id.push(i+1);
rowObj.end.push(i + 2);
rowObj.chr.push("epiviz");
}
return rowObj;
}
}
}
</script>