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Flekschas/overlay tracks 1d and 2d (#524)
* Remove commented out logs and add a warning for SVG export * Prettify code style * Allow setting fill opacity * Enable 1d vertical overlays * Determin orientation from track position to support overlays of combined tracks * Added an example * Add a simple base test for overlay tracks * Extend base test * Remove log
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| { | ||
| "editable": true, | ||
| "zoomFixed": false, | ||
| "trackSourceServers": ["http://higlass.io/api/v1"], | ||
| "exportViewUrl": "http://localhost:8000/api/v1/viewconfs/", | ||
| "views": [{ | ||
| "uid": "aa", | ||
| "initialXDomain": [-128227010, 3227095876], | ||
| "initialYDomain": [-679063376, 3737688490], | ||
| "autocompleteSource": "http://higlass.io/api/v1/suggest/?d=OHJakQICQD6gTD7skx4EWA&", | ||
| "genomePositionSearchBoxVisible": false, | ||
| "chromInfoPath": "//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv", | ||
| "tracks": { | ||
| "top": [{ | ||
| "server": "http://higlass.io/api/v1", | ||
| "tilesetUid": "OHJakQICQD6gTD7skx4EWA", | ||
| "uid": "genes-top", | ||
| "type": "horizontal-gene-annotations" | ||
| }, { | ||
| "chromInfoPath": "//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv", | ||
| "type": "horizontal-chromosome-labels", | ||
| "position": "top", | ||
| "uid": "chroms-top" | ||
| }], | ||
| "left": [{ | ||
| "server": "http://higlass.io/api/v1", | ||
| "tilesetUid": "OHJakQICQD6gTD7skx4EWA", | ||
| "uid": "genes-left", | ||
| "type": "vertical-gene-annotations" | ||
| }, { | ||
| "chromInfoPath": "//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv", | ||
| "type": "vertical-chromosome-labels", | ||
| "position": "left", | ||
| "name": "Chromosome Labels (hg19)", | ||
| "uid": "chroms-left" | ||
| }], | ||
| "center": [{ | ||
| "uid": "center", | ||
| "type": "combined", | ||
| "contents": [{ | ||
| "data": { | ||
| "type": "divided", | ||
| "children": [{ | ||
| "server": "http://higlass.io/api/v1", | ||
| "tilesetUid": "CQMd6V_cRw6iCI_-Unl3PQ" | ||
| }, { | ||
| "server": "http://higlass.io/api/v1", | ||
| "tilesetUid": "ZCvntCKST0KUvQPGcCbJGA" | ||
| }] | ||
| }, | ||
| "type": "heatmap", | ||
| "position": "center", | ||
| "options": { | ||
| "colorRange": ["#FFFFFF", "#F8E71C", "#F5A623", "#D0021B"], | ||
| "colorbarPosition": "topRight", | ||
| "colorbarLabelsPosition": "outside", | ||
| "maxZoom": null, | ||
| "labelPosition": "bottomLeft", | ||
| "name": "Rao et al. (2014) GM12878 MboI (allreps) 1kb", | ||
| "trackBorderWidth": 0, | ||
| "trackBorderColor": "black", | ||
| "heatmapValueScaling": "log", | ||
| "scaleStartPercent": "0.00000", | ||
| "scaleEndPercent": "1.00000" | ||
| }, | ||
| "uid": "heatmap", | ||
| "name": "Rao et al. (2014) GM12878 MboI (allreps) 1kb", | ||
| "transforms": [{ | ||
| "name": "ICE", | ||
| "value": "weight" | ||
| }] | ||
| }, { | ||
| "type": "2d-chromosome-grid", | ||
| "chromInfoPath": "//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv", | ||
| "tilesetUid": "TIlwFtqxTX-ndtM7Y9k1bw", | ||
| "uid": "LUVqXXu2QYiO8XURIwyUyA", | ||
| "options": { | ||
| "lineStrokeWidth": 1, | ||
| "lineStrokeColor": "grey" | ||
| } | ||
| }] | ||
| }], | ||
| "right": [], | ||
| "bottom": [] | ||
| }, | ||
| "layout": { | ||
| "w": 12, | ||
| "h": 12, | ||
| "x": 0, | ||
| "y": 0, | ||
| "i": "aa", | ||
| "moved": false, | ||
| "static": false | ||
| }, | ||
| "overlays": [{ | ||
| "uid": "overlay", | ||
| "type": "", | ||
| "includes": ["chroms-top", "chroms-left", "genes-top", "genes-left", "center"], | ||
| "options": { | ||
| "extent": [ | ||
| [1000000000, 1100000000] | ||
| ] | ||
| } | ||
| }] | ||
| }] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,66 @@ | ||
| /* eslint-env node, jasmine */ | ||
|
|
||
| // Utils | ||
| // import { | ||
| // getTrackObjectFromHGC, | ||
| // waitForTilesLoaded | ||
| // } from '../app/scripts/utils'; | ||
|
|
||
| import createElementAndApi from './utils/create-element-and-api'; | ||
| import removeDiv from './utils/remove-div'; | ||
|
|
||
| import overlayAnnotations1d2dViewConf from './view-configs/overlay-annotations-1d-2d'; | ||
|
|
||
| describe('Overlay Track:', () => { | ||
| let hgc = null; | ||
| let api = null; | ||
| let div = null; | ||
| let viewConf; | ||
|
|
||
| describe('Annotation overlays:', () => { | ||
| it('Should render', (done) => { | ||
| viewConf = overlayAnnotations1d2dViewConf; | ||
|
|
||
| [div, api] = createElementAndApi(viewConf, { bound: true }); | ||
|
|
||
| hgc = api.getComponent(); | ||
|
|
||
| const numNormalTracks = viewConf.views[0].tracks.top.length | ||
| + viewConf.views[0].tracks.right.length | ||
| + viewConf.views[0].tracks.bottom.length | ||
| + viewConf.views[0].tracks.left.length | ||
| + viewConf.views[0].tracks.center.length; | ||
|
|
||
| expect(numNormalTracks).toEqual(4); | ||
|
|
||
| const trackRenderer = hgc.tiledPlots[viewConf.views[0].uid] | ||
| .trackRenderer; | ||
|
|
||
| const posTracks = trackRenderer.props.positionedTracks; | ||
|
|
||
| expect(posTracks.length).toEqual(5); | ||
|
|
||
| const overlayTrack = posTracks[posTracks.length - 1]; | ||
|
|
||
| expect(overlayTrack.track.type).toEqual('overlay-track'); | ||
|
|
||
| const overlayTrackInfo = trackRenderer | ||
| .trackDefObjects[overlayTrack.track.uid]; | ||
|
|
||
| const overlayTrackDef = overlayTrackInfo.trackDef; | ||
| const overlayTrackObj = overlayTrackInfo.trackObject; | ||
|
|
||
| expect(overlayTrackDef.width).toEqual(overlayTrackObj.dimensions[0]); | ||
| expect(overlayTrackDef.height).toEqual(overlayTrackObj.dimensions[1]); | ||
|
|
||
| done(); | ||
| }); | ||
|
|
||
| afterEach(() => { | ||
| if (api && api.destroy) api.destroy(); | ||
| if (div) removeDiv(div); | ||
| api = undefined; | ||
| div = undefined; | ||
| }); | ||
| }); | ||
| }); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| const viewConf = { | ||
| editable: false, | ||
| zoomFixed: false, | ||
| views: [{ | ||
| uid: 'aa', | ||
| initialXDomain: [-128227010, 3227095876], | ||
| tracks: { | ||
| top: [ | ||
| { | ||
| server: 'http://higlass.io/api/v1', | ||
| tilesetUid: 'OHJakQICQD6gTD7skx4EWA', | ||
| uid: 'genes-top', | ||
| type: 'horizontal-gene-annotations' | ||
| }, | ||
| { | ||
| chromInfoPath: '//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv', | ||
| type: 'horizontal-chromosome-labels', | ||
| position: 'top', | ||
| uid: 'chroms-top' | ||
| } | ||
| ], | ||
| left: [ | ||
| { | ||
| server: 'http://higlass.io/api/v1', | ||
| tilesetUid: 'OHJakQICQD6gTD7skx4EWA', | ||
| uid: 'genes-left', | ||
| type: 'vertical-gene-annotations' | ||
| }, | ||
| { | ||
| chromInfoPath: '//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv', | ||
| type: 'vertical-chromosome-labels', | ||
| position: 'left', | ||
| name: 'Chromosome Labels (hg19)', | ||
| uid: 'chroms-left' | ||
| } | ||
| ], | ||
| center: [], | ||
| right: [], | ||
| bottom: [] | ||
| }, | ||
| layout: { | ||
| w: 12, | ||
| h: 12, | ||
| x: 0, | ||
| y: 0, | ||
| i: 'aa', | ||
| moved: false, | ||
| static: false | ||
| }, | ||
| overlays: [{ | ||
| uid: 'overlay', | ||
| type: '', | ||
| includes: ['chroms-top', 'chroms-left', 'genes-top', 'genes-left'], | ||
| options: { | ||
| extent: [ | ||
| [1000000000, 1100000000] | ||
| ] | ||
| } | ||
| }] | ||
| }] | ||
| }; | ||
|
|
||
| export default viewConf; |