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Added an option for only showing whole interactions
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@pkerpedjiev
pkerpedjiev committed Nov 14, 2020
1 parent 1556e8b commit 211c465
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Showing 2 changed files with 131 additions and 175 deletions.
29 changes: 29 additions & 0 deletions src/Arcs1DTrack.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -171,6 +171,20 @@ const Arcs1DTrack = (HGC, ...args) => {
for (let i = 0; i < items.length; i++) {
const item = items[i];

if (this.options.completelyContained) {
const x1 = this._xScale(
item.xStart || item.chrOffset + item.fields[1]
);
const x2 = this._xScale(
item.xEnd || item.chrOffset + item.fields[2]
);

if (x1 < this._xScale.range()[0] || x2 > this._xScale.range()[1]) {
// one end of this
continue;
}
}

if (this.options.arcStyle === 'circle') {
this.drawCircle(tile.graphics, item, opacityScale, storePolyStr);
} else {
Expand Down Expand Up @@ -265,6 +279,7 @@ Arcs1DTrack.config = {
thumbnail: new DOMParser().parseFromString(icon, 'text/xml').documentElement,
availableOptions: [
'arcStyle',
'completelyContained',
'flip1D',
'labelPosition',
'labelColor',
Expand All @@ -278,6 +293,7 @@ Arcs1DTrack.config = {
],
defaultOptions: {
arcStyle: 'ellipse',
completelyContained: false,
flip1D: 'no',
labelColor: 'black',
labelPosition: 'hidden',
Expand All @@ -301,6 +317,19 @@ Arcs1DTrack.config = {
},
},
},
completelyContained: {
name: 'Only whole interactions',
inlineOptions: {
yes: {
name: 'Yes',
value: true,
},
no: {
name: 'No',
value: false,
},
},
},
},
};

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277 changes: 102 additions & 175 deletions src/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -26,215 +26,142 @@
const testViewConfig =
{
"editable": true,
"trackSourceServers": [
"/api/v1",
"http://higlass.io/api/v1"
],
"exportViewUrl": "/api/v1/viewconfs",
"views": [
{
"uid": "bq8XqbKnSByCds_LNA0KPw",
"initialXDomain": [
1894256531.2007055,
1895066338.1494255
],
"initialYDomain": [
1894723774.199916,
1895073759.7317762
],
"tracks": {
"top": [
{
"type": "top-axis",
"options": {},
"uid": "T-h45lNeRsez_jv6rD9izg",
"server": "http://localhost:50478/api/v1",
"height": 20
},
{
"type": "horizontal-chromosome-labels",
"options": {
"tickPositions": "ends",
"color": "#808080",
"stroke": "#ffffff",
"fontSize": 12,
"fontIsLeftAligned": false,
"showMousePosition": false,
"mousePositionColor": "#000000"
},
"tilesetUid": "ADfY_RtsQR6oKOMyrq6qhw",
"height": 30,
"width": null,
"server": "https://resgen.io/api/v1",
"uid": "LL6t70pOQWWmn9IVmicKSg"
},
{
"type": "horizontal-gene-annotations",
"options": {
"fontSize": 10,
"labelColor": "black",
"labelBackgroundColor": "#ffffff",
"labelPosition": "hidden",
"labelLeftMargin": 0,
"labelRightMargin": 0,
"labelTopMargin": 0,
"labelBottomMargin": 0,
"minHeight": 24,
"plusStrandColor": "blue",
"minusStrandColor": "red",
"trackBorderWidth": 0,
"trackBorderColor": "black",
"showMousePosition": false,
"mousePositionColor": "#000000",
"geneAnnotationHeight": 12,
"geneLabelPosition": "outside",
"geneStrandSpacing": 4,
"name": "Gene Annotations (hg19)"
},
"tilesetUid": "NCifnbrKQu6j-ohVWJLoJw",
"height": 55,
"width": null,
"server": "https://resgen.io/api/v1",
"uid": "etN9kTVxTe6jn5O8uZ6Oow"
},
{
"type": "horizontal-bar",
"options": {
"barFillColor": "rgb(201, 99, 95)",
"align": "bottom",
"labelColor": "[glyph-color]",
"labelPosition": "topLeft",
"labelLeftMargin": 0,
"labelRightMargin": 0,
"labelTopMargin": 0,
"labelBottomMargin": 0,
"labelShowResolution": false,
"axisLabelFormatting": "scientific",
"axisPositionHorizontal": "right",
"valueScaling": "linear",
"trackBorderWidth": 0,
"trackBorderColor": "black",
"labelTextOpacity": 0.4,
"barOpacity": 1,
"name": "microglia_H3K27ac_pooled"
},
"tilesetUid": "WyTmNKusQyuFmVmpSpPzCQ",
"height": 20,
"width": null,
"server": "https://resgen.io/api/v1",
"uid": "V3SfNozTRsCmKw3aU3XLPQ",
"aggregationModes": {
"mean": {
"name": "Mean",
"value": "mean"
},
"min": {
"name": "Min",
"value": "min"
},
"max": {
"name": "Max",
"value": "max"
},
"std": {
"name": "Standard Deviation",
"value": "std"
"uid": "YxaUPlcZTMKzEh1X_vXOWw",
"type": "combined",
"contents": [
{
"type": "chromosome-labels",
"uid": "PTMVt-w0RSCkvgT_hP1OIA",
"tilesetUid": "ZpZ8c5JJRUS1J7ZkofcUrg",
"server": "https://resgen.io/api/v1",
"options": {
"color": "#808080",
"stroke": "#ffffff",
"fontSize": 12,
"fontIsLeftAligned": false,
"showMousePosition": false,
"mousePositionColor": "#000000"
},
"width": 20,
"height": 30
}
}
],
"height": 30,
"options": {}
},
{
"type": "1d-arcs",
"options": {
"labelPosition": "topLeft",
"strokeColor": "green",
"strokeWidth": 1,
"arcStyle": "circle",
"flip1D": "yes",
"labelColor": "black",
"trackBorderWidth": 0,
"trackBorderColor": "black",
"name": "Neuron PLAC-seq"
},
"tilesetUid": "JzccFAJUQEiz-0188xaWZg",
"height": 50,
"width": null,
"server": "https://resgen.io/api/v1",
"uid": "KZU7cwYbQdmrFNRTK85IQg",
"aggregationModes": {
"mean": {
"name": "Mean",
"value": "mean"
},
"min": {
"name": "Min",
"value": "min"
},
"max": {
"name": "Max",
"value": "max"
},
"std": {
"name": "Standard Deviation",
"value": "std"
"uid": "bUzzq7CrSxab2hVfgLBIUA",
"type": "combined",
"contents": [
{
"type": "horizontal-gene-annotations",
"uid": "KKgLx1hvRAac1SMM2xzKAg",
"tilesetUid": "M9A9klpwTci5Vf4bHZ864g",
"server": "https://resgen.io/api/v1",
"options": {
"fontSize": 10,
"labelColor": "black",
"labelBackgroundColor": "#ffffff",
"labelPosition": "hidden",
"labelLeftMargin": 0,
"labelRightMargin": 0,
"labelTopMargin": 0,
"labelBottomMargin": 0,
"minHeight": 24,
"plusStrandColor": "blue",
"minusStrandColor": "red",
"trackBorderWidth": 0,
"trackBorderColor": "black",
"showMousePosition": false,
"mousePositionColor": "#000000",
"geneAnnotationHeight": 16,
"geneLabelPosition": "outside",
"geneStrandSpacing": 4,
"name": "Gene Annotations (hg38)"
},
"width": 909,
"height": 90
}
}
],
"height": 90,
"options": {}
},
{
"type": "1d-arcs",
"options": {
"labelPosition": "topLeft",
"strokeColor": "green",
"strokeWidth": 1,
"arcStyle": "circle",
"flip1D": "no",
"labelColor": "black",
"trackBorderWidth": 0,
"trackBorderColor": "black",
"name": "Neuron PLAC-seq"
},
"tilesetUid": "JzccFAJUQEiz-0188xaWZg",
"height": 50,
"width": null,
"server": "https://resgen.io/api/v1",
"uid": "u2",
"aggregationModes": {
"mean": {
"name": "Mean",
"value": "mean"
},
"min": {
"name": "Min",
"value": "min"
},
"max": {
"name": "Max",
"value": "max"
},
"std": {
"name": "Standard Deviation",
"value": "std"
"uid": "B8aJmt5aRGCiNv0nntPBnA",
"type": "combined",
"contents": [
{
"type": "1d-arcs",
"uid": "GfyU7X6OSUa_iB0LB61HYQ",
"tilesetUid": "AD5M_uwCS2uMCdUr9rj8qA",
"server": "https://resgen.io/api/v1",
"options": {
"arcStyle": "ellipse",
"flip1D": "no",
"labelColor": "black",
"labelPosition": "hidden",
"completelyContained": true,
"strokeColor": "black",
"strokeOpacity": 0.12,
"strokeWidth": 1,
"trackBorderWidth": 0,
"trackBorderColor": "black",
"name": "corces_interactions_bedified.bgz"
},
"width": 909,
"height": 240
}
}
],
"height": 240,
"options": {}
}
],
"center": [],
"left": [],
"right": [],
"center": [],
"bottom": [],
"right": [],
"whole": [],
"gallery": []
},
"layout": {
"w": 12,
"h": 12,
"h": 6,
"x": 0,
"y": 0
},
"initialXDomain": [2460667111, 2461667111],
"initialYDomain": [2461167111, 2461167111]
"uid": "V-Nxxb97SbK5XClWvpRMFw"
}
],
"trackSourceServers": ["http://higlass.io/api/v1"],
"locationLocks": {
"zoomLocks": {
"locksByViewUid": {},
"locksDict": {}
},
"valueScaleLocks": {
"locationLocks": {
"locksByViewUid": {},
"locksDict": {}
},
"zoomLocks": {
"valueScaleLocks": {
"locksByViewUid": {},
"locksDict": {}
},
"exportViewUrl": "http://higlass.io/api/v1/viewconfs"
}
}


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