@sjcrh/proteinpaint-client 2.191.4 → 2.192.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/2dmaf-BNMEUJVM.js +1373 -0
- package/dist/AIProjectAdmin-AEXQY5LY.js +958 -0
- package/dist/AIProjectAdmin-AEXQY5LY.js.map +7 -0
- package/dist/AppHeader-RXDJBHXZ.js +835 -0
- package/dist/BoxPlot-HDP3SIGU.js +1217 -0
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- package/dist/CorrelationVolcano-V2E566XL.js +619 -0
- package/dist/DE-7YUZSW4E.js +95 -0
- package/dist/DEinput-P2HOQC4Z.js +301 -0
- package/dist/DifferentialAnalysis-2Z6BHS7A.js +245 -0
- package/dist/Disco-ZLC54X7T.js +3297 -0
- package/dist/Disco-ZLC54X7T.js.map +7 -0
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- package/dist/DmrPlot-OEJRGNI3.js +642 -0
- package/dist/GB-2GHDD3MW.js +1130 -0
- package/dist/GeneExpInput-PWLPDLYT.js +367 -0
- package/dist/GeneExpInput-PWLPDLYT.js.map +7 -0
- package/dist/HicApp-CAYC4DPO.js +2250 -0
- package/dist/NumBinaryEditor-EUOYSGPM.js +271 -0
- package/dist/NumBinaryEditor.unit.spec-5B3W4B4F.js +286 -0
- package/dist/NumContEditor-7KK6CIB3.js +109 -0
- package/dist/NumContEditor.unit.spec-IMKGVYFZ.js +169 -0
- package/dist/NumCustomBinEditor-PDAF6I7B.js +38 -0
- package/dist/NumCustomBinEditor.unit.spec-IU3DPECJ.js +284 -0
- package/dist/NumDiscreteEditor-YTKUHG6Z.js +179 -0
- package/dist/NumDiscreteEditor.unit.spec-FUBS7Z7Z.js +202 -0
- package/dist/NumRegularBinEditor-LU3KLBLY.js +38 -0
- package/dist/NumRegularBinEditor.unit.spec-2BKOHI7L.js +227 -0
- package/dist/NumSplineEditor-56RJ2HT2.js +198 -0
- package/dist/NumSplineEditor.unit.spec-PW6VUUBZ.js +199 -0
- package/dist/NumericDensity-EB4H54EF.js +38 -0
- package/dist/NumericDensity.unit.spec-LSEM4OEY.js +221 -0
- package/dist/NumericHandler-VGPDXP35.js +39 -0
- package/dist/NumericHandler.unit.spec-NR3F7XHV.js +219 -0
- package/dist/ProteomeInput-AUXWUIWK.js +396 -0
- package/dist/RunChart2-SQ6TFOHD.js +758 -0
- package/dist/SC-OWJ6LYIW.js +1124 -0
- package/dist/SC-OWJ6LYIW.js.map +7 -0
- package/dist/Volcano-XHDH6UN7.js +1379 -0
- package/dist/WSIViewer-WT2QV747.js +48562 -0
- package/dist/WSIViewer-WT2QV747.js.map +7 -0
- package/dist/WsiSamplesPlot-YUOAWG2A.js +165 -0
- package/dist/adSandbox-VMMAL22L.js +38 -0
- package/dist/animatedBubbleChart-Q6Z5W2UL.js +555 -0
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- package/dist/app-FX3KZ67X.js +37 -0
- package/dist/app-X7ZYEOZN.js +49 -0
- package/dist/app.js +20 -20
- package/dist/bam-ZYLH4U5R.js +860 -0
- package/dist/barchart-MXSPTKV4.js +47 -0
- package/dist/barchart.data-ZWF6EVJH.js +22 -0
- package/dist/barchart.events-XON2ANOC.js +47 -0
- package/dist/barchart.integration.spec-PJIENJGT.js +1980 -0
- package/dist/barchart2-HIKBGSSE.js +314 -0
- package/dist/barchart2-HIKBGSSE.js.map +7 -0
- package/dist/bars.renderer-57KSYAAT.js +12 -0
- package/dist/block-EGPYVWNP.js +6226 -0
- package/dist/block-EGPYVWNP.js.map +7 -0
- package/dist/block.init-IJBRPZNM.js +38 -0
- package/dist/block.mds.expressionrank-3DANCP7E.js +359 -0
- package/dist/block.mds.geneboxplot-CRGSCZMG.js +828 -0
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- package/dist/block.tk.bedgraphdot-MYHKKO6K.js +384 -0
- package/dist/block.tk.bigwig.ui-E3YVGIDN.js +212 -0
- package/dist/block.tk.hicstraw-Y4XOMG7T.js +823 -0
- package/dist/block.tk.junction-T5C7LK6F.js +2364 -0
- package/dist/block.tk.junction.textmatrixui-Z3ACCVXH.js +199 -0
- package/dist/block.tk.ld-Y5KDA5AU.js +99 -0
- package/dist/block.tk.menu-EWRRISDY.js +1029 -0
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- package/dist/brainImaging-P3AF3C5N.js +423 -0
- package/dist/brainRegions-YA2H2QOI.js +221 -0
- package/dist/brainRegions-YA2H2QOI.js.map +7 -0
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- package/dist/dataDownload-SOUCBKXM.js +330 -0
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- package/dist/dictionary-RUT5VXDD.js +118 -0
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- package/dist/dnaMethylation-WOKGG33W.js +38 -0
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197
|
-
PCDheader2.count = [];
|
|
198
|
-
for (let i = 0, l = PCDheader2.fields.length; i < l; i++) {
|
|
199
|
-
PCDheader2.count.push(1);
|
|
200
|
-
}
|
|
201
|
-
}
|
|
202
|
-
PCDheader2.offset = {};
|
|
203
|
-
let sizeSum = 0;
|
|
204
|
-
for (let i = 0, l = PCDheader2.fields.length; i < l; i++) {
|
|
205
|
-
if (PCDheader2.data === "ascii") {
|
|
206
|
-
PCDheader2.offset[PCDheader2.fields[i]] = i;
|
|
207
|
-
} else {
|
|
208
|
-
PCDheader2.offset[PCDheader2.fields[i]] = sizeSum;
|
|
209
|
-
sizeSum += PCDheader2.size[i] * PCDheader2.count[i];
|
|
210
|
-
}
|
|
211
|
-
}
|
|
212
|
-
PCDheader2.rowSize = sizeSum;
|
|
213
|
-
return PCDheader2;
|
|
214
|
-
}
|
|
215
|
-
const textData = new TextDecoder().decode(data);
|
|
216
|
-
const PCDheader = parseHeader(textData);
|
|
217
|
-
const position = [];
|
|
218
|
-
const normal = [];
|
|
219
|
-
const color = [];
|
|
220
|
-
const intensity = [];
|
|
221
|
-
const label = [];
|
|
222
|
-
if (PCDheader.data === "ascii") {
|
|
223
|
-
const offset = PCDheader.offset;
|
|
224
|
-
const pcdData = textData.slice(PCDheader.headerLen);
|
|
225
|
-
const lines = pcdData.split("\n");
|
|
226
|
-
for (let i = 0, l = lines.length; i < l; i++) {
|
|
227
|
-
if (lines[i] === "") continue;
|
|
228
|
-
const line = lines[i].split(" ");
|
|
229
|
-
if (offset.x !== void 0) {
|
|
230
|
-
position.push(parseFloat(line[offset.x]));
|
|
231
|
-
position.push(parseFloat(line[offset.y]));
|
|
232
|
-
position.push(parseFloat(line[offset.z]));
|
|
233
|
-
}
|
|
234
|
-
if (offset.rgb !== void 0) {
|
|
235
|
-
const rgb_field_index = PCDheader.fields.findIndex((field) => field === "rgb");
|
|
236
|
-
const rgb_type = PCDheader.type[rgb_field_index];
|
|
237
|
-
const float = parseFloat(line[offset.rgb]);
|
|
238
|
-
let rgb = float;
|
|
239
|
-
if (rgb_type === "F") {
|
|
240
|
-
const farr = new Float32Array(1);
|
|
241
|
-
farr[0] = float;
|
|
242
|
-
rgb = new Int32Array(farr.buffer)[0];
|
|
243
|
-
}
|
|
244
|
-
const r = rgb >> 16 & 255;
|
|
245
|
-
const g = rgb >> 8 & 255;
|
|
246
|
-
const b = rgb >> 0 & 255;
|
|
247
|
-
color.push(r / 255, g / 255, b / 255);
|
|
248
|
-
}
|
|
249
|
-
if (offset.normal_x !== void 0) {
|
|
250
|
-
normal.push(parseFloat(line[offset.normal_x]));
|
|
251
|
-
normal.push(parseFloat(line[offset.normal_y]));
|
|
252
|
-
normal.push(parseFloat(line[offset.normal_z]));
|
|
253
|
-
}
|
|
254
|
-
if (offset.intensity !== void 0) {
|
|
255
|
-
intensity.push(parseFloat(line[offset.intensity]));
|
|
256
|
-
}
|
|
257
|
-
if (offset.label !== void 0) {
|
|
258
|
-
label.push(parseInt(line[offset.label]));
|
|
259
|
-
}
|
|
260
|
-
}
|
|
261
|
-
}
|
|
262
|
-
if (PCDheader.data === "binary_compressed") {
|
|
263
|
-
const sizes = new Uint32Array(data.slice(PCDheader.headerLen, PCDheader.headerLen + 8));
|
|
264
|
-
const compressedSize = sizes[0];
|
|
265
|
-
const decompressedSize = sizes[1];
|
|
266
|
-
const decompressed = decompressLZF(new Uint8Array(data, PCDheader.headerLen + 8, compressedSize), decompressedSize);
|
|
267
|
-
const dataview = new DataView(decompressed.buffer);
|
|
268
|
-
const offset = PCDheader.offset;
|
|
269
|
-
for (let i = 0; i < PCDheader.points; i++) {
|
|
270
|
-
if (offset.x !== void 0) {
|
|
271
|
-
const xIndex = PCDheader.fields.indexOf("x");
|
|
272
|
-
const yIndex = PCDheader.fields.indexOf("y");
|
|
273
|
-
const zIndex = PCDheader.fields.indexOf("z");
|
|
274
|
-
position.push(dataview.getFloat32(PCDheader.points * offset.x + PCDheader.size[xIndex] * i, this.littleEndian));
|
|
275
|
-
position.push(dataview.getFloat32(PCDheader.points * offset.y + PCDheader.size[yIndex] * i, this.littleEndian));
|
|
276
|
-
position.push(dataview.getFloat32(PCDheader.points * offset.z + PCDheader.size[zIndex] * i, this.littleEndian));
|
|
277
|
-
}
|
|
278
|
-
if (offset.rgb !== void 0) {
|
|
279
|
-
const rgbIndex = PCDheader.fields.indexOf("rgb");
|
|
280
|
-
color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[rgbIndex] * i + 2) / 255);
|
|
281
|
-
color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[rgbIndex] * i + 1) / 255);
|
|
282
|
-
color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[rgbIndex] * i + 0) / 255);
|
|
283
|
-
}
|
|
284
|
-
if (offset.normal_x !== void 0) {
|
|
285
|
-
const xIndex = PCDheader.fields.indexOf("normal_x");
|
|
286
|
-
const yIndex = PCDheader.fields.indexOf("normal_y");
|
|
287
|
-
const zIndex = PCDheader.fields.indexOf("normal_z");
|
|
288
|
-
normal.push(dataview.getFloat32(PCDheader.points * offset.normal_x + PCDheader.size[xIndex] * i, this.littleEndian));
|
|
289
|
-
normal.push(dataview.getFloat32(PCDheader.points * offset.normal_y + PCDheader.size[yIndex] * i, this.littleEndian));
|
|
290
|
-
normal.push(dataview.getFloat32(PCDheader.points * offset.normal_z + PCDheader.size[zIndex] * i, this.littleEndian));
|
|
291
|
-
}
|
|
292
|
-
if (offset.intensity !== void 0) {
|
|
293
|
-
const intensityIndex = PCDheader.fields.indexOf("intensity");
|
|
294
|
-
intensity.push(dataview.getFloat32(PCDheader.points * offset.intensity + PCDheader.size[intensityIndex] * i, this.littleEndian));
|
|
295
|
-
}
|
|
296
|
-
if (offset.label !== void 0) {
|
|
297
|
-
const labelIndex = PCDheader.fields.indexOf("label");
|
|
298
|
-
label.push(dataview.getInt32(PCDheader.points * offset.label + PCDheader.size[labelIndex] * i, this.littleEndian));
|
|
299
|
-
}
|
|
300
|
-
}
|
|
301
|
-
}
|
|
302
|
-
if (PCDheader.data === "binary") {
|
|
303
|
-
const dataview = new DataView(data, PCDheader.headerLen);
|
|
304
|
-
const offset = PCDheader.offset;
|
|
305
|
-
for (let i = 0, row = 0; i < PCDheader.points; i++, row += PCDheader.rowSize) {
|
|
306
|
-
if (offset.x !== void 0) {
|
|
307
|
-
position.push(dataview.getFloat32(row + offset.x, this.littleEndian));
|
|
308
|
-
position.push(dataview.getFloat32(row + offset.y, this.littleEndian));
|
|
309
|
-
position.push(dataview.getFloat32(row + offset.z, this.littleEndian));
|
|
310
|
-
}
|
|
311
|
-
if (offset.rgb !== void 0) {
|
|
312
|
-
color.push(dataview.getUint8(row + offset.rgb + 2) / 255);
|
|
313
|
-
color.push(dataview.getUint8(row + offset.rgb + 1) / 255);
|
|
314
|
-
color.push(dataview.getUint8(row + offset.rgb + 0) / 255);
|
|
315
|
-
}
|
|
316
|
-
if (offset.normal_x !== void 0) {
|
|
317
|
-
normal.push(dataview.getFloat32(row + offset.normal_x, this.littleEndian));
|
|
318
|
-
normal.push(dataview.getFloat32(row + offset.normal_y, this.littleEndian));
|
|
319
|
-
normal.push(dataview.getFloat32(row + offset.normal_z, this.littleEndian));
|
|
320
|
-
}
|
|
321
|
-
if (offset.intensity !== void 0) {
|
|
322
|
-
intensity.push(dataview.getFloat32(row + offset.intensity, this.littleEndian));
|
|
323
|
-
}
|
|
324
|
-
if (offset.label !== void 0) {
|
|
325
|
-
label.push(dataview.getInt32(row + offset.label, this.littleEndian));
|
|
326
|
-
}
|
|
327
|
-
}
|
|
328
|
-
}
|
|
329
|
-
const geometry = new BufferGeometry();
|
|
330
|
-
if (position.length > 0) geometry.setAttribute("position", new Float32BufferAttribute(position, 3));
|
|
331
|
-
if (normal.length > 0) geometry.setAttribute("normal", new Float32BufferAttribute(normal, 3));
|
|
332
|
-
if (color.length > 0) geometry.setAttribute("color", new Float32BufferAttribute(color, 3));
|
|
333
|
-
if (intensity.length > 0) geometry.setAttribute("intensity", new Float32BufferAttribute(intensity, 1));
|
|
334
|
-
if (label.length > 0) geometry.setAttribute("label", new Int32BufferAttribute(label, 1));
|
|
335
|
-
geometry.computeBoundingSphere();
|
|
336
|
-
const material = new PointsMaterial({ size: 5e-3 });
|
|
337
|
-
if (color.length > 0) {
|
|
338
|
-
material.vertexColors = true;
|
|
339
|
-
}
|
|
340
|
-
return new Points(geometry, material);
|
|
341
|
-
}
|
|
342
|
-
};
|
|
343
|
-
|
|
344
|
-
// ../public/static/js/WebGL.js
|
|
345
|
-
function isWebGLAvailable() {
|
|
346
|
-
try {
|
|
347
|
-
var canvas = document.createElement("canvas");
|
|
348
|
-
return !!(window.WebGLRenderingContext && (canvas.getContext("webgl") || canvas.getContext("experimental-webgl")));
|
|
349
|
-
} catch (e) {
|
|
350
|
-
return false;
|
|
351
|
-
}
|
|
352
|
-
}
|
|
353
|
-
function getWebGLErrorMessage() {
|
|
354
|
-
return this.getErrorMessage(1);
|
|
355
|
-
}
|
|
356
|
-
|
|
357
|
-
// ../node_modules/three/examples/jsm/controls/TrackballControls.js
|
|
358
|
-
var _changeEvent = { type: "change" };
|
|
359
|
-
var _startEvent = { type: "start" };
|
|
360
|
-
var _endEvent = { type: "end" };
|
|
361
|
-
var TrackballControls = class extends EventDispatcher {
|
|
362
|
-
constructor(object, domElement) {
|
|
363
|
-
super();
|
|
364
|
-
const scope = this;
|
|
365
|
-
const STATE = { NONE: -1, ROTATE: 0, ZOOM: 1, PAN: 2, TOUCH_ROTATE: 3, TOUCH_ZOOM_PAN: 4 };
|
|
366
|
-
this.object = object;
|
|
367
|
-
this.domElement = domElement;
|
|
368
|
-
this.domElement.style.touchAction = "none";
|
|
369
|
-
this.enabled = true;
|
|
370
|
-
this.screen = { left: 0, top: 0, width: 0, height: 0 };
|
|
371
|
-
this.rotateSpeed = 1;
|
|
372
|
-
this.zoomSpeed = 1.2;
|
|
373
|
-
this.panSpeed = 0.3;
|
|
374
|
-
this.noRotate = false;
|
|
375
|
-
this.noZoom = false;
|
|
376
|
-
this.noPan = false;
|
|
377
|
-
this.staticMoving = false;
|
|
378
|
-
this.dynamicDampingFactor = 0.2;
|
|
379
|
-
this.minDistance = 0;
|
|
380
|
-
this.maxDistance = Infinity;
|
|
381
|
-
this.minZoom = 0;
|
|
382
|
-
this.maxZoom = Infinity;
|
|
383
|
-
this.keys = [
|
|
384
|
-
"KeyA",
|
|
385
|
-
"KeyS",
|
|
386
|
-
"KeyD"
|
|
387
|
-
/*D*/
|
|
388
|
-
];
|
|
389
|
-
this.mouseButtons = { LEFT: MOUSE.ROTATE, MIDDLE: MOUSE.DOLLY, RIGHT: MOUSE.PAN };
|
|
390
|
-
this.target = new Vector3();
|
|
391
|
-
const EPS = 1e-6;
|
|
392
|
-
const lastPosition = new Vector3();
|
|
393
|
-
let lastZoom = 1;
|
|
394
|
-
let _state = STATE.NONE, _keyState = STATE.NONE, _touchZoomDistanceStart = 0, _touchZoomDistanceEnd = 0, _lastAngle = 0;
|
|
395
|
-
const _eye = new Vector3(), _movePrev = new Vector2(), _moveCurr = new Vector2(), _lastAxis = new Vector3(), _zoomStart = new Vector2(), _zoomEnd = new Vector2(), _panStart = new Vector2(), _panEnd = new Vector2(), _pointers = [], _pointerPositions = {};
|
|
396
|
-
this.target0 = this.target.clone();
|
|
397
|
-
this.position0 = this.object.position.clone();
|
|
398
|
-
this.up0 = this.object.up.clone();
|
|
399
|
-
this.zoom0 = this.object.zoom;
|
|
400
|
-
this.handleResize = function() {
|
|
401
|
-
const box = scope.domElement.getBoundingClientRect();
|
|
402
|
-
const d = scope.domElement.ownerDocument.documentElement;
|
|
403
|
-
scope.screen.left = box.left + window.pageXOffset - d.clientLeft;
|
|
404
|
-
scope.screen.top = box.top + window.pageYOffset - d.clientTop;
|
|
405
|
-
scope.screen.width = box.width;
|
|
406
|
-
scope.screen.height = box.height;
|
|
407
|
-
};
|
|
408
|
-
const getMouseOnScreen = (function() {
|
|
409
|
-
const vector = new Vector2();
|
|
410
|
-
return function getMouseOnScreen2(pageX, pageY) {
|
|
411
|
-
vector.set(
|
|
412
|
-
(pageX - scope.screen.left) / scope.screen.width,
|
|
413
|
-
(pageY - scope.screen.top) / scope.screen.height
|
|
414
|
-
);
|
|
415
|
-
return vector;
|
|
416
|
-
};
|
|
417
|
-
})();
|
|
418
|
-
const getMouseOnCircle = (function() {
|
|
419
|
-
const vector = new Vector2();
|
|
420
|
-
return function getMouseOnCircle2(pageX, pageY) {
|
|
421
|
-
vector.set(
|
|
422
|
-
(pageX - scope.screen.width * 0.5 - scope.screen.left) / (scope.screen.width * 0.5),
|
|
423
|
-
(scope.screen.height + 2 * (scope.screen.top - pageY)) / scope.screen.width
|
|
424
|
-
// screen.width intentional
|
|
425
|
-
);
|
|
426
|
-
return vector;
|
|
427
|
-
};
|
|
428
|
-
})();
|
|
429
|
-
this.rotateCamera = (function() {
|
|
430
|
-
const axis = new Vector3(), quaternion = new Quaternion(), eyeDirection = new Vector3(), objectUpDirection = new Vector3(), objectSidewaysDirection = new Vector3(), moveDirection = new Vector3();
|
|
431
|
-
return function rotateCamera() {
|
|
432
|
-
moveDirection.set(_moveCurr.x - _movePrev.x, _moveCurr.y - _movePrev.y, 0);
|
|
433
|
-
let angle = moveDirection.length();
|
|
434
|
-
if (angle) {
|
|
435
|
-
_eye.copy(scope.object.position).sub(scope.target);
|
|
436
|
-
eyeDirection.copy(_eye).normalize();
|
|
437
|
-
objectUpDirection.copy(scope.object.up).normalize();
|
|
438
|
-
objectSidewaysDirection.crossVectors(objectUpDirection, eyeDirection).normalize();
|
|
439
|
-
objectUpDirection.setLength(_moveCurr.y - _movePrev.y);
|
|
440
|
-
objectSidewaysDirection.setLength(_moveCurr.x - _movePrev.x);
|
|
441
|
-
moveDirection.copy(objectUpDirection.add(objectSidewaysDirection));
|
|
442
|
-
axis.crossVectors(moveDirection, _eye).normalize();
|
|
443
|
-
angle *= scope.rotateSpeed;
|
|
444
|
-
quaternion.setFromAxisAngle(axis, angle);
|
|
445
|
-
_eye.applyQuaternion(quaternion);
|
|
446
|
-
scope.object.up.applyQuaternion(quaternion);
|
|
447
|
-
_lastAxis.copy(axis);
|
|
448
|
-
_lastAngle = angle;
|
|
449
|
-
} else if (!scope.staticMoving && _lastAngle) {
|
|
450
|
-
_lastAngle *= Math.sqrt(1 - scope.dynamicDampingFactor);
|
|
451
|
-
_eye.copy(scope.object.position).sub(scope.target);
|
|
452
|
-
quaternion.setFromAxisAngle(_lastAxis, _lastAngle);
|
|
453
|
-
_eye.applyQuaternion(quaternion);
|
|
454
|
-
scope.object.up.applyQuaternion(quaternion);
|
|
455
|
-
}
|
|
456
|
-
_movePrev.copy(_moveCurr);
|
|
457
|
-
};
|
|
458
|
-
})();
|
|
459
|
-
this.zoomCamera = function() {
|
|
460
|
-
let factor;
|
|
461
|
-
if (_state === STATE.TOUCH_ZOOM_PAN) {
|
|
462
|
-
factor = _touchZoomDistanceStart / _touchZoomDistanceEnd;
|
|
463
|
-
_touchZoomDistanceStart = _touchZoomDistanceEnd;
|
|
464
|
-
if (scope.object.isPerspectiveCamera) {
|
|
465
|
-
_eye.multiplyScalar(factor);
|
|
466
|
-
} else if (scope.object.isOrthographicCamera) {
|
|
467
|
-
scope.object.zoom = MathUtils.clamp(scope.object.zoom / factor, scope.minZoom, scope.maxZoom);
|
|
468
|
-
if (lastZoom !== scope.object.zoom) {
|
|
469
|
-
scope.object.updateProjectionMatrix();
|
|
470
|
-
}
|
|
471
|
-
} else {
|
|
472
|
-
console.warn("THREE.TrackballControls: Unsupported camera type");
|
|
473
|
-
}
|
|
474
|
-
} else {
|
|
475
|
-
factor = 1 + (_zoomEnd.y - _zoomStart.y) * scope.zoomSpeed;
|
|
476
|
-
if (factor !== 1 && factor > 0) {
|
|
477
|
-
if (scope.object.isPerspectiveCamera) {
|
|
478
|
-
_eye.multiplyScalar(factor);
|
|
479
|
-
} else if (scope.object.isOrthographicCamera) {
|
|
480
|
-
scope.object.zoom = MathUtils.clamp(scope.object.zoom / factor, scope.minZoom, scope.maxZoom);
|
|
481
|
-
if (lastZoom !== scope.object.zoom) {
|
|
482
|
-
scope.object.updateProjectionMatrix();
|
|
483
|
-
}
|
|
484
|
-
} else {
|
|
485
|
-
console.warn("THREE.TrackballControls: Unsupported camera type");
|
|
486
|
-
}
|
|
487
|
-
}
|
|
488
|
-
if (scope.staticMoving) {
|
|
489
|
-
_zoomStart.copy(_zoomEnd);
|
|
490
|
-
} else {
|
|
491
|
-
_zoomStart.y += (_zoomEnd.y - _zoomStart.y) * this.dynamicDampingFactor;
|
|
492
|
-
}
|
|
493
|
-
}
|
|
494
|
-
};
|
|
495
|
-
this.panCamera = (function() {
|
|
496
|
-
const mouseChange = new Vector2(), objectUp = new Vector3(), pan = new Vector3();
|
|
497
|
-
return function panCamera() {
|
|
498
|
-
mouseChange.copy(_panEnd).sub(_panStart);
|
|
499
|
-
if (mouseChange.lengthSq()) {
|
|
500
|
-
if (scope.object.isOrthographicCamera) {
|
|
501
|
-
const scale_x = (scope.object.right - scope.object.left) / scope.object.zoom / scope.domElement.clientWidth;
|
|
502
|
-
const scale_y = (scope.object.top - scope.object.bottom) / scope.object.zoom / scope.domElement.clientWidth;
|
|
503
|
-
mouseChange.x *= scale_x;
|
|
504
|
-
mouseChange.y *= scale_y;
|
|
505
|
-
}
|
|
506
|
-
mouseChange.multiplyScalar(_eye.length() * scope.panSpeed);
|
|
507
|
-
pan.copy(_eye).cross(scope.object.up).setLength(mouseChange.x);
|
|
508
|
-
pan.add(objectUp.copy(scope.object.up).setLength(mouseChange.y));
|
|
509
|
-
scope.object.position.add(pan);
|
|
510
|
-
scope.target.add(pan);
|
|
511
|
-
if (scope.staticMoving) {
|
|
512
|
-
_panStart.copy(_panEnd);
|
|
513
|
-
} else {
|
|
514
|
-
_panStart.add(mouseChange.subVectors(_panEnd, _panStart).multiplyScalar(scope.dynamicDampingFactor));
|
|
515
|
-
}
|
|
516
|
-
}
|
|
517
|
-
};
|
|
518
|
-
})();
|
|
519
|
-
this.checkDistances = function() {
|
|
520
|
-
if (!scope.noZoom || !scope.noPan) {
|
|
521
|
-
if (_eye.lengthSq() > scope.maxDistance * scope.maxDistance) {
|
|
522
|
-
scope.object.position.addVectors(scope.target, _eye.setLength(scope.maxDistance));
|
|
523
|
-
_zoomStart.copy(_zoomEnd);
|
|
524
|
-
}
|
|
525
|
-
if (_eye.lengthSq() < scope.minDistance * scope.minDistance) {
|
|
526
|
-
scope.object.position.addVectors(scope.target, _eye.setLength(scope.minDistance));
|
|
527
|
-
_zoomStart.copy(_zoomEnd);
|
|
528
|
-
}
|
|
529
|
-
}
|
|
530
|
-
};
|
|
531
|
-
this.update = function() {
|
|
532
|
-
_eye.subVectors(scope.object.position, scope.target);
|
|
533
|
-
if (!scope.noRotate) {
|
|
534
|
-
scope.rotateCamera();
|
|
535
|
-
}
|
|
536
|
-
if (!scope.noZoom) {
|
|
537
|
-
scope.zoomCamera();
|
|
538
|
-
}
|
|
539
|
-
if (!scope.noPan) {
|
|
540
|
-
scope.panCamera();
|
|
541
|
-
}
|
|
542
|
-
scope.object.position.addVectors(scope.target, _eye);
|
|
543
|
-
if (scope.object.isPerspectiveCamera) {
|
|
544
|
-
scope.checkDistances();
|
|
545
|
-
scope.object.lookAt(scope.target);
|
|
546
|
-
if (lastPosition.distanceToSquared(scope.object.position) > EPS) {
|
|
547
|
-
scope.dispatchEvent(_changeEvent);
|
|
548
|
-
lastPosition.copy(scope.object.position);
|
|
549
|
-
}
|
|
550
|
-
} else if (scope.object.isOrthographicCamera) {
|
|
551
|
-
scope.object.lookAt(scope.target);
|
|
552
|
-
if (lastPosition.distanceToSquared(scope.object.position) > EPS || lastZoom !== scope.object.zoom) {
|
|
553
|
-
scope.dispatchEvent(_changeEvent);
|
|
554
|
-
lastPosition.copy(scope.object.position);
|
|
555
|
-
lastZoom = scope.object.zoom;
|
|
556
|
-
}
|
|
557
|
-
} else {
|
|
558
|
-
console.warn("THREE.TrackballControls: Unsupported camera type");
|
|
559
|
-
}
|
|
560
|
-
};
|
|
561
|
-
this.reset = function() {
|
|
562
|
-
_state = STATE.NONE;
|
|
563
|
-
_keyState = STATE.NONE;
|
|
564
|
-
scope.target.copy(scope.target0);
|
|
565
|
-
scope.object.position.copy(scope.position0);
|
|
566
|
-
scope.object.up.copy(scope.up0);
|
|
567
|
-
scope.object.zoom = scope.zoom0;
|
|
568
|
-
scope.object.updateProjectionMatrix();
|
|
569
|
-
_eye.subVectors(scope.object.position, scope.target);
|
|
570
|
-
scope.object.lookAt(scope.target);
|
|
571
|
-
scope.dispatchEvent(_changeEvent);
|
|
572
|
-
lastPosition.copy(scope.object.position);
|
|
573
|
-
lastZoom = scope.object.zoom;
|
|
574
|
-
};
|
|
575
|
-
function onPointerDown(event) {
|
|
576
|
-
if (scope.enabled === false) return;
|
|
577
|
-
if (_pointers.length === 0) {
|
|
578
|
-
scope.domElement.setPointerCapture(event.pointerId);
|
|
579
|
-
scope.domElement.addEventListener("pointermove", onPointerMove);
|
|
580
|
-
scope.domElement.addEventListener("pointerup", onPointerUp);
|
|
581
|
-
}
|
|
582
|
-
addPointer(event);
|
|
583
|
-
if (event.pointerType === "touch") {
|
|
584
|
-
onTouchStart(event);
|
|
585
|
-
} else {
|
|
586
|
-
onMouseDown(event);
|
|
587
|
-
}
|
|
588
|
-
}
|
|
589
|
-
function onPointerMove(event) {
|
|
590
|
-
if (scope.enabled === false) return;
|
|
591
|
-
if (event.pointerType === "touch") {
|
|
592
|
-
onTouchMove(event);
|
|
593
|
-
} else {
|
|
594
|
-
onMouseMove(event);
|
|
595
|
-
}
|
|
596
|
-
}
|
|
597
|
-
function onPointerUp(event) {
|
|
598
|
-
if (scope.enabled === false) return;
|
|
599
|
-
if (event.pointerType === "touch") {
|
|
600
|
-
onTouchEnd(event);
|
|
601
|
-
} else {
|
|
602
|
-
onMouseUp();
|
|
603
|
-
}
|
|
604
|
-
removePointer(event);
|
|
605
|
-
if (_pointers.length === 0) {
|
|
606
|
-
scope.domElement.releasePointerCapture(event.pointerId);
|
|
607
|
-
scope.domElement.removeEventListener("pointermove", onPointerMove);
|
|
608
|
-
scope.domElement.removeEventListener("pointerup", onPointerUp);
|
|
609
|
-
}
|
|
610
|
-
}
|
|
611
|
-
function onPointerCancel(event) {
|
|
612
|
-
removePointer(event);
|
|
613
|
-
}
|
|
614
|
-
function keydown(event) {
|
|
615
|
-
if (scope.enabled === false) return;
|
|
616
|
-
window.removeEventListener("keydown", keydown);
|
|
617
|
-
if (_keyState !== STATE.NONE) {
|
|
618
|
-
return;
|
|
619
|
-
} else if (event.code === scope.keys[STATE.ROTATE] && !scope.noRotate) {
|
|
620
|
-
_keyState = STATE.ROTATE;
|
|
621
|
-
} else if (event.code === scope.keys[STATE.ZOOM] && !scope.noZoom) {
|
|
622
|
-
_keyState = STATE.ZOOM;
|
|
623
|
-
} else if (event.code === scope.keys[STATE.PAN] && !scope.noPan) {
|
|
624
|
-
_keyState = STATE.PAN;
|
|
625
|
-
}
|
|
626
|
-
}
|
|
627
|
-
function keyup() {
|
|
628
|
-
if (scope.enabled === false) return;
|
|
629
|
-
_keyState = STATE.NONE;
|
|
630
|
-
window.addEventListener("keydown", keydown);
|
|
631
|
-
}
|
|
632
|
-
function onMouseDown(event) {
|
|
633
|
-
if (_state === STATE.NONE) {
|
|
634
|
-
switch (event.button) {
|
|
635
|
-
case scope.mouseButtons.LEFT:
|
|
636
|
-
_state = STATE.ROTATE;
|
|
637
|
-
break;
|
|
638
|
-
case scope.mouseButtons.MIDDLE:
|
|
639
|
-
_state = STATE.ZOOM;
|
|
640
|
-
break;
|
|
641
|
-
case scope.mouseButtons.RIGHT:
|
|
642
|
-
_state = STATE.PAN;
|
|
643
|
-
break;
|
|
644
|
-
}
|
|
645
|
-
}
|
|
646
|
-
const state = _keyState !== STATE.NONE ? _keyState : _state;
|
|
647
|
-
if (state === STATE.ROTATE && !scope.noRotate) {
|
|
648
|
-
_moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
|
|
649
|
-
_movePrev.copy(_moveCurr);
|
|
650
|
-
} else if (state === STATE.ZOOM && !scope.noZoom) {
|
|
651
|
-
_zoomStart.copy(getMouseOnScreen(event.pageX, event.pageY));
|
|
652
|
-
_zoomEnd.copy(_zoomStart);
|
|
653
|
-
} else if (state === STATE.PAN && !scope.noPan) {
|
|
654
|
-
_panStart.copy(getMouseOnScreen(event.pageX, event.pageY));
|
|
655
|
-
_panEnd.copy(_panStart);
|
|
656
|
-
}
|
|
657
|
-
scope.dispatchEvent(_startEvent);
|
|
658
|
-
}
|
|
659
|
-
function onMouseMove(event) {
|
|
660
|
-
const state = _keyState !== STATE.NONE ? _keyState : _state;
|
|
661
|
-
if (state === STATE.ROTATE && !scope.noRotate) {
|
|
662
|
-
_movePrev.copy(_moveCurr);
|
|
663
|
-
_moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
|
|
664
|
-
} else if (state === STATE.ZOOM && !scope.noZoom) {
|
|
665
|
-
_zoomEnd.copy(getMouseOnScreen(event.pageX, event.pageY));
|
|
666
|
-
} else if (state === STATE.PAN && !scope.noPan) {
|
|
667
|
-
_panEnd.copy(getMouseOnScreen(event.pageX, event.pageY));
|
|
668
|
-
}
|
|
669
|
-
}
|
|
670
|
-
function onMouseUp() {
|
|
671
|
-
_state = STATE.NONE;
|
|
672
|
-
scope.dispatchEvent(_endEvent);
|
|
673
|
-
}
|
|
674
|
-
function onMouseWheel(event) {
|
|
675
|
-
if (scope.enabled === false) return;
|
|
676
|
-
if (scope.noZoom === true) return;
|
|
677
|
-
event.preventDefault();
|
|
678
|
-
switch (event.deltaMode) {
|
|
679
|
-
case 2:
|
|
680
|
-
_zoomStart.y -= event.deltaY * 0.025;
|
|
681
|
-
break;
|
|
682
|
-
case 1:
|
|
683
|
-
_zoomStart.y -= event.deltaY * 0.01;
|
|
684
|
-
break;
|
|
685
|
-
default:
|
|
686
|
-
_zoomStart.y -= event.deltaY * 25e-5;
|
|
687
|
-
break;
|
|
688
|
-
}
|
|
689
|
-
scope.dispatchEvent(_startEvent);
|
|
690
|
-
scope.dispatchEvent(_endEvent);
|
|
691
|
-
}
|
|
692
|
-
function onTouchStart(event) {
|
|
693
|
-
trackPointer(event);
|
|
694
|
-
switch (_pointers.length) {
|
|
695
|
-
case 1:
|
|
696
|
-
_state = STATE.TOUCH_ROTATE;
|
|
697
|
-
_moveCurr.copy(getMouseOnCircle(_pointers[0].pageX, _pointers[0].pageY));
|
|
698
|
-
_movePrev.copy(_moveCurr);
|
|
699
|
-
break;
|
|
700
|
-
default:
|
|
701
|
-
_state = STATE.TOUCH_ZOOM_PAN;
|
|
702
|
-
const dx = _pointers[0].pageX - _pointers[1].pageX;
|
|
703
|
-
const dy = _pointers[0].pageY - _pointers[1].pageY;
|
|
704
|
-
_touchZoomDistanceEnd = _touchZoomDistanceStart = Math.sqrt(dx * dx + dy * dy);
|
|
705
|
-
const x = (_pointers[0].pageX + _pointers[1].pageX) / 2;
|
|
706
|
-
const y = (_pointers[0].pageY + _pointers[1].pageY) / 2;
|
|
707
|
-
_panStart.copy(getMouseOnScreen(x, y));
|
|
708
|
-
_panEnd.copy(_panStart);
|
|
709
|
-
break;
|
|
710
|
-
}
|
|
711
|
-
scope.dispatchEvent(_startEvent);
|
|
712
|
-
}
|
|
713
|
-
function onTouchMove(event) {
|
|
714
|
-
trackPointer(event);
|
|
715
|
-
switch (_pointers.length) {
|
|
716
|
-
case 1:
|
|
717
|
-
_movePrev.copy(_moveCurr);
|
|
718
|
-
_moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
|
|
719
|
-
break;
|
|
720
|
-
default:
|
|
721
|
-
const position = getSecondPointerPosition(event);
|
|
722
|
-
const dx = event.pageX - position.x;
|
|
723
|
-
const dy = event.pageY - position.y;
|
|
724
|
-
_touchZoomDistanceEnd = Math.sqrt(dx * dx + dy * dy);
|
|
725
|
-
const x = (event.pageX + position.x) / 2;
|
|
726
|
-
const y = (event.pageY + position.y) / 2;
|
|
727
|
-
_panEnd.copy(getMouseOnScreen(x, y));
|
|
728
|
-
break;
|
|
729
|
-
}
|
|
730
|
-
}
|
|
731
|
-
function onTouchEnd(event) {
|
|
732
|
-
switch (_pointers.length) {
|
|
733
|
-
case 0:
|
|
734
|
-
_state = STATE.NONE;
|
|
735
|
-
break;
|
|
736
|
-
case 1:
|
|
737
|
-
_state = STATE.TOUCH_ROTATE;
|
|
738
|
-
_moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
|
|
739
|
-
_movePrev.copy(_moveCurr);
|
|
740
|
-
break;
|
|
741
|
-
case 2:
|
|
742
|
-
_state = STATE.TOUCH_ZOOM_PAN;
|
|
743
|
-
for (let i = 0; i < _pointers.length; i++) {
|
|
744
|
-
if (_pointers[i].pointerId !== event.pointerId) {
|
|
745
|
-
const position = _pointerPositions[_pointers[i].pointerId];
|
|
746
|
-
_moveCurr.copy(getMouseOnCircle(position.x, position.y));
|
|
747
|
-
_movePrev.copy(_moveCurr);
|
|
748
|
-
break;
|
|
749
|
-
}
|
|
750
|
-
}
|
|
751
|
-
break;
|
|
752
|
-
}
|
|
753
|
-
scope.dispatchEvent(_endEvent);
|
|
754
|
-
}
|
|
755
|
-
function contextmenu(event) {
|
|
756
|
-
if (scope.enabled === false) return;
|
|
757
|
-
event.preventDefault();
|
|
758
|
-
}
|
|
759
|
-
function addPointer(event) {
|
|
760
|
-
_pointers.push(event);
|
|
761
|
-
}
|
|
762
|
-
function removePointer(event) {
|
|
763
|
-
delete _pointerPositions[event.pointerId];
|
|
764
|
-
for (let i = 0; i < _pointers.length; i++) {
|
|
765
|
-
if (_pointers[i].pointerId == event.pointerId) {
|
|
766
|
-
_pointers.splice(i, 1);
|
|
767
|
-
return;
|
|
768
|
-
}
|
|
769
|
-
}
|
|
770
|
-
}
|
|
771
|
-
function trackPointer(event) {
|
|
772
|
-
let position = _pointerPositions[event.pointerId];
|
|
773
|
-
if (position === void 0) {
|
|
774
|
-
position = new Vector2();
|
|
775
|
-
_pointerPositions[event.pointerId] = position;
|
|
776
|
-
}
|
|
777
|
-
position.set(event.pageX, event.pageY);
|
|
778
|
-
}
|
|
779
|
-
function getSecondPointerPosition(event) {
|
|
780
|
-
const pointer = event.pointerId === _pointers[0].pointerId ? _pointers[1] : _pointers[0];
|
|
781
|
-
return _pointerPositions[pointer.pointerId];
|
|
782
|
-
}
|
|
783
|
-
this.dispose = function() {
|
|
784
|
-
scope.domElement.removeEventListener("contextmenu", contextmenu);
|
|
785
|
-
scope.domElement.removeEventListener("pointerdown", onPointerDown);
|
|
786
|
-
scope.domElement.removeEventListener("pointercancel", onPointerCancel);
|
|
787
|
-
scope.domElement.removeEventListener("wheel", onMouseWheel);
|
|
788
|
-
scope.domElement.removeEventListener("pointermove", onPointerMove);
|
|
789
|
-
scope.domElement.removeEventListener("pointerup", onPointerUp);
|
|
790
|
-
window.removeEventListener("keydown", keydown);
|
|
791
|
-
window.removeEventListener("keyup", keyup);
|
|
792
|
-
};
|
|
793
|
-
this.domElement.addEventListener("contextmenu", contextmenu);
|
|
794
|
-
this.domElement.addEventListener("pointerdown", onPointerDown);
|
|
795
|
-
this.domElement.addEventListener("pointercancel", onPointerCancel);
|
|
796
|
-
this.domElement.addEventListener("wheel", onMouseWheel, { passive: false });
|
|
797
|
-
window.addEventListener("keydown", keydown);
|
|
798
|
-
window.addEventListener("keyup", keyup);
|
|
799
|
-
this.handleResize();
|
|
800
|
-
this.update();
|
|
801
|
-
}
|
|
802
|
-
};
|
|
803
|
-
|
|
804
|
-
// src/singlecell.js
|
|
805
|
-
async function init(arg, holder) {
|
|
806
|
-
try {
|
|
807
|
-
const obj = await load_json(arg);
|
|
808
|
-
validate_obj(obj);
|
|
809
|
-
obj.genome = arg.genome;
|
|
810
|
-
obj.holder = holder.style("position", "relative");
|
|
811
|
-
await init_view(obj);
|
|
812
|
-
init_controlpanel(obj);
|
|
813
|
-
await pcd_pipeline(obj);
|
|
814
|
-
make_legend(arg, obj);
|
|
815
|
-
} catch (e) {
|
|
816
|
-
sayerror(holder, e.message || e);
|
|
817
|
-
}
|
|
818
|
-
}
|
|
819
|
-
async function load_json(arg) {
|
|
820
|
-
if (!arg.jsonfile) throw ".jsonfile missing";
|
|
821
|
-
const tmp = await dofetch("textfile", { file: arg.jsonfile });
|
|
822
|
-
if (tmp.error) throw tmp.error;
|
|
823
|
-
return JSON.parse(tmp.text);
|
|
824
|
-
}
|
|
825
|
-
function validate_obj(obj) {
|
|
826
|
-
if (!obj.cells) throw ".cells{} missing";
|
|
827
|
-
if (!obj.cells.file) throw ".cells.file missing";
|
|
828
|
-
if (!obj.cells.axis2columnidx) throw ".cells.axis2columnidx missing";
|
|
829
|
-
if (obj.cells.categories) {
|
|
830
|
-
if (!Array.isArray(obj.cells.categories)) throw ".cells.categories should be an array";
|
|
831
|
-
if (obj.cells.categories.length == 0) throw ".cells.categories[] is empty array";
|
|
832
|
-
for (const c of obj.cells.categories) {
|
|
833
|
-
if (!Number.isInteger(c.columnidx)) throw "columnidx missing from category " + c;
|
|
834
|
-
if (c.autocolor) {
|
|
835
|
-
c.autocolor = ordinal(schemeCategory20);
|
|
836
|
-
}
|
|
837
|
-
}
|
|
838
|
-
if (!Number.isInteger(obj.use_category_index)) {
|
|
839
|
-
obj.use_category_index = 0;
|
|
840
|
-
}
|
|
841
|
-
if (!obj.cells.categories[obj.use_category_index]) throw "use_category_index out of bound";
|
|
842
|
-
if (!obj.cells.categories[obj.use_category_index].hidden_types)
|
|
843
|
-
obj.cells.categories[obj.use_category_index].hidden_types = [];
|
|
844
|
-
}
|
|
845
|
-
if (obj.gene_expression) {
|
|
846
|
-
if (!obj.gene_expression.file) throw ".gene_expression.file missing";
|
|
847
|
-
if (!Number.isInteger(obj.cells.barcodecolumnidx))
|
|
848
|
-
throw ".gene_expression in use but .cells.barcodecolumnidx is missing";
|
|
849
|
-
}
|
|
850
|
-
if (!obj.width) obj.width = window.innerWidth * 0.9;
|
|
851
|
-
if (!obj.height) obj.height = window.innerHeight * 0.9;
|
|
852
|
-
}
|
|
853
|
-
async function pcd_pipeline(obj) {
|
|
854
|
-
if (Number.isInteger(obj.use_category_index)) {
|
|
855
|
-
if (!obj.cells.categories[obj.use_category_index].hidden_types)
|
|
856
|
-
obj.cells.categories[obj.use_category_index].hidden_types = [];
|
|
857
|
-
}
|
|
858
|
-
const data = await load_cell_pcd(obj);
|
|
859
|
-
obj.data_sphere_r = data.data_sphere_r;
|
|
860
|
-
if (!obj.camera.position.z) {
|
|
861
|
-
obj.camera.position.z = obj.data_sphere_r * 3;
|
|
862
|
-
obj.controls.maxDistance = obj.data_sphere_r * 4;
|
|
863
|
-
obj.controls.minDistance = obj.data_sphere_r / 10;
|
|
864
|
-
}
|
|
865
|
-
const enc = new TextEncoder();
|
|
866
|
-
const pcd_buffer = enc.encode(data.pcddata).buffer;
|
|
867
|
-
render_cloud(obj, pcd_buffer);
|
|
868
|
-
render_controlpanel(obj, data);
|
|
869
|
-
animate();
|
|
870
|
-
function animate() {
|
|
871
|
-
requestAnimationFrame(animate);
|
|
872
|
-
obj.controls.update();
|
|
873
|
-
obj.renderer.render(obj.scene, obj.camera);
|
|
874
|
-
}
|
|
875
|
-
}
|
|
876
|
-
async function load_cell_pcd(obj) {
|
|
877
|
-
const wait = obj.holder.append("div").style("position", "absolute").style("top", 0).style("left", 0).style("padding", "10px").style("font-size", "1.5rem").text("Loading data...");
|
|
878
|
-
const arg = {
|
|
879
|
-
genome: obj.genome.name,
|
|
880
|
-
textfile: obj.cells.file,
|
|
881
|
-
delimiter: obj.cells.delimiter || " ",
|
|
882
|
-
getpcd: {
|
|
883
|
-
coord: obj.cells.axis2columnidx
|
|
884
|
-
}
|
|
885
|
-
};
|
|
886
|
-
if (Number.isInteger(obj.use_category_index)) {
|
|
887
|
-
if (!obj.cells.categories) throw "using category index but cells.categories[] missing";
|
|
888
|
-
const cat = obj.cells.categories[obj.use_category_index];
|
|
889
|
-
if (!cat) throw "category array index out of bound";
|
|
890
|
-
arg.getpcd.category_index = cat.columnidx;
|
|
891
|
-
if (cat.autocolor) {
|
|
892
|
-
arg.getpcd.category_autocolor = true;
|
|
893
|
-
if (cat.values_count) arg.getpcd.values_count = cat.values_count;
|
|
894
|
-
} else if (cat.values) {
|
|
895
|
-
arg.getpcd.category_customcolor = true;
|
|
896
|
-
arg.getpcd.cat_values = cat.values;
|
|
897
|
-
} else {
|
|
898
|
-
if (!cat.autocolor && !cat.values) throw "categories.values[] are not defined";
|
|
899
|
-
throw "unknow coloring scheme for category " + cat.name;
|
|
900
|
-
}
|
|
901
|
-
if (cat.hidden_types) {
|
|
902
|
-
arg.hidden_types = cat.hidden_types;
|
|
903
|
-
}
|
|
904
|
-
if (obj.background_color) {
|
|
905
|
-
arg.background_color = obj.background_color;
|
|
906
|
-
}
|
|
907
|
-
if (!cat.customorder) {
|
|
908
|
-
arg.getpcd.category_autoorder = true;
|
|
909
|
-
} else if (cat.customorder && cat.values) {
|
|
910
|
-
arg.getpcd.category_customorder = true;
|
|
911
|
-
arg.getpcd.cat_values = cat.values;
|
|
912
|
-
} else {
|
|
913
|
-
if (cat.customorder && !cat.values) throw "categories.values[] are not defined";
|
|
914
|
-
throw "unknow ordering scheme for category " + cat.name;
|
|
915
|
-
}
|
|
916
|
-
obj.menu_button.html(cat.name + " ▼");
|
|
917
|
-
} else if (Number.isInteger(obj.use_gene_index)) {
|
|
918
|
-
const gene = obj.gene_expression.genes[obj.use_gene_index];
|
|
919
|
-
obj.menu_button.html("Gene : " + gene.gene + " ▼");
|
|
920
|
-
arg.getpcd.gene_expression = {
|
|
921
|
-
file: obj.gene_expression.file,
|
|
922
|
-
barcodecolumnidx: obj.cells.barcodecolumnidx,
|
|
923
|
-
chr: gene.chr,
|
|
924
|
-
start: gene.start,
|
|
925
|
-
stop: gene.stop,
|
|
926
|
-
autoscale: true,
|
|
927
|
-
genename: gene.gene,
|
|
928
|
-
color_min: obj.gene_expression.color_min,
|
|
929
|
-
color_max: obj.gene_expression.color_max
|
|
930
|
-
};
|
|
931
|
-
if (obj.gene_expression.color_no_exp) arg.getpcd.gene_expression.color_no_exp = obj.gene_expression.color_no_exp;
|
|
932
|
-
} else {
|
|
933
|
-
throw "unknown method to color the cells";
|
|
934
|
-
}
|
|
935
|
-
return dofetch("singlecell", arg).then((data) => {
|
|
936
|
-
if (data.error) throw data.error;
|
|
937
|
-
wait.remove();
|
|
938
|
-
return data;
|
|
939
|
-
});
|
|
940
|
-
}
|
|
941
|
-
async function init_view(obj) {
|
|
942
|
-
if (isWebGLAvailable() === false) {
|
|
943
|
-
obj.holder.node().appendChild(getWebGLErrorMessage());
|
|
944
|
-
return;
|
|
945
|
-
}
|
|
946
|
-
obj.scene = new Scene();
|
|
947
|
-
if (obj.background_color) {
|
|
948
|
-
obj.scene.background = new Color(obj.background_color);
|
|
949
|
-
} else {
|
|
950
|
-
obj.scene.background = new Color(16777215);
|
|
951
|
-
}
|
|
952
|
-
const default_zoom = obj.default_zoom ? 100 - obj.default_zoom : 45;
|
|
953
|
-
obj.camera = new PerspectiveCamera(default_zoom, obj.width / obj.height, 0.1, 1e3);
|
|
954
|
-
obj.camera.position.x = obj.canvas_2d ? 0 : 20;
|
|
955
|
-
obj.camera.position.y = obj.canvas_2d ? 0 : -10;
|
|
956
|
-
if (obj.canvas_2d) {
|
|
957
|
-
obj.camera.up.set(0, 1, 0);
|
|
958
|
-
} else {
|
|
959
|
-
obj.camera.up.set(0, 0, 1);
|
|
960
|
-
}
|
|
961
|
-
obj.renderer = new WebGLRenderer({ antialias: true, preserveDrawingBuffer: true });
|
|
962
|
-
obj.renderer.setPixelRatio(window.devicePixelRatio);
|
|
963
|
-
obj.renderer.setSize(obj.width, obj.height);
|
|
964
|
-
obj.renderer.domElement.style.backgroundColor = "#ffffff";
|
|
965
|
-
obj.renderer.domElement.style.border = "solid #dddddd 2px";
|
|
966
|
-
obj.renderer.outputColorSpace = LinearSRGBColorSpace;
|
|
967
|
-
obj.renderer.toneMapping = NoToneMapping;
|
|
968
|
-
obj.holder.style("display", "inline-block").style("position", "relative").node().appendChild(obj.renderer.domElement);
|
|
969
|
-
obj.controls = new TrackballControls(obj.camera, obj.renderer.domElement);
|
|
970
|
-
obj.controls.rotateSpeed = obj.canvas_2d ? 0 : 2;
|
|
971
|
-
obj.controls.zoomSpeed = obj.canvas_2d ? 3 : 0.7;
|
|
972
|
-
obj.controls.panSpeed = obj.canvas_2d ? 3 : 0.7;
|
|
973
|
-
obj.controls.noZoom = true;
|
|
974
|
-
obj.controls.noPan = false;
|
|
975
|
-
obj.controls.staticMoving = true;
|
|
976
|
-
obj.controls.dynamicDampingFactor = 0.3;
|
|
977
|
-
obj.scene.add(obj.camera);
|
|
978
|
-
obj.renderer.render(obj.scene, obj.camera);
|
|
979
|
-
obj.controls.update();
|
|
980
|
-
}
|
|
981
|
-
function render_cloud(obj, pcd_buffer) {
|
|
982
|
-
obj.scene.children.forEach(function(v, i) {
|
|
983
|
-
if (v.material) {
|
|
984
|
-
v.material.dispose();
|
|
985
|
-
v.geometry.dispose();
|
|
986
|
-
obj.scene.remove(v);
|
|
987
|
-
}
|
|
988
|
-
});
|
|
989
|
-
const loader = new PCDLoader();
|
|
990
|
-
const points = loader.parse(pcd_buffer, "");
|
|
991
|
-
const newMat = new PointsMaterial({
|
|
992
|
-
size: points.material.size,
|
|
993
|
-
vertexColors: true,
|
|
994
|
-
color: 16777215
|
|
995
|
-
});
|
|
996
|
-
points.material = newMat;
|
|
997
|
-
points.material.vertexColors = true;
|
|
998
|
-
points.material.color.set(16777215);
|
|
999
|
-
points.material.needsUpdate = true;
|
|
1000
|
-
if (obj.point_size) {
|
|
1001
|
-
points.material.size = obj.point_size;
|
|
1002
|
-
} else {
|
|
1003
|
-
points.material.size = obj.canvas_2d ? 0.3 : 0.05;
|
|
1004
|
-
}
|
|
1005
|
-
obj.scene.add(points);
|
|
1006
|
-
obj.center = points.geometry.boundingSphere.center;
|
|
1007
|
-
obj.controls.target.set(obj.center.x, obj.center.y, obj.center.z);
|
|
1008
|
-
obj.controls.update();
|
|
1009
|
-
}
|
|
1010
|
-
function init_controlpanel(obj) {
|
|
1011
|
-
obj.menu = new Menu();
|
|
1012
|
-
obj.menu.d.style("padding", "3px");
|
|
1013
|
-
obj.settings = new Menu();
|
|
1014
|
-
obj.settings.d.style("padding", "3px");
|
|
1015
|
-
const panel = obj.holder.append("div").style("padding", "10px").style("position", "absolute").style("border-radius", "5px").style("top", "20px").style("right", "20px").style("background-color", "#dddddd");
|
|
1016
|
-
obj.menu_button = panel.append("button").style("display", "inline-block").style("padding", "4px").on("click", () => make_menu(obj));
|
|
1017
|
-
const minimize_btn = obj.minimize_btn = panel.append("div").style("margin-left", "10px").style("display", "inline-block").style("padding-left", "0px").style("padding-right", "2px").style("float", "right").style("font-size", ".6em").classed("active", obj.menu_minimized ? true : false).text(obj.menu_minimized ? " SHOW" : " HIDE").on("click", () => {
|
|
1018
|
-
obj.minimize_btn.classed("active", obj.minimize_btn.classed("active") ? false : true);
|
|
1019
|
-
if (obj.minimize_btn.classed("active")) {
|
|
1020
|
-
obj.minimize_btn.text(" SHOW");
|
|
1021
|
-
obj.menu_output.style("display", "none");
|
|
1022
|
-
} else {
|
|
1023
|
-
obj.minimize_btn.text(" HIDE");
|
|
1024
|
-
obj.menu_output.style("display", "block");
|
|
1025
|
-
}
|
|
1026
|
-
}).on("mouseover", () => {
|
|
1027
|
-
minimize_btn.style("text-decoration", "underline");
|
|
1028
|
-
}).on("mouseout", () => {
|
|
1029
|
-
minimize_btn.style("text-decoration", "none");
|
|
1030
|
-
});
|
|
1031
|
-
obj.use_background_color = 0;
|
|
1032
|
-
const config_btn = obj.settings_btn = panel.append("div").style("margin-left", "10px").style("display", "inline-block").style("padding-left", "3px").style("padding-right", "3px").style("float", "right").style("font-size", ".6em").text("CONFIG").on("click", () => make_settings(obj)).on("mouseover", () => {
|
|
1033
|
-
config_btn.style("text-decoration", "underline");
|
|
1034
|
-
}).on("mouseout", () => {
|
|
1035
|
-
config_btn.style("text-decoration", "none");
|
|
1036
|
-
});
|
|
1037
|
-
obj.menu_output = panel.append("div").style("margin-top", "10px").style("display", obj.menu_minimized ? "none" : "block");
|
|
1038
|
-
obj.show_zoom = true;
|
|
1039
|
-
}
|
|
1040
|
-
function render_controlpanel(obj, data) {
|
|
1041
|
-
obj.menu_output.selectAll("*").remove();
|
|
1042
|
-
if (data.category2color) {
|
|
1043
|
-
const top_row = obj.menu_output.append("div").style("margin", "2px");
|
|
1044
|
-
const select_all_checkbox = top_row.append("input").attr("type", "checkbox").style("margin-right", "10px").style("vertical-align", "top").style("display", "inline-block").on("change", () => {
|
|
1045
|
-
if (select_all_checkbox.node().checked) {
|
|
1046
|
-
obj.cells.categories[obj.use_category_index].hidden_types = [];
|
|
1047
|
-
pcd_pipeline(obj);
|
|
1048
|
-
} else {
|
|
1049
|
-
for (const type in data.category2color) {
|
|
1050
|
-
obj.cells.categories[obj.use_category_index].hidden_types.push(type);
|
|
1051
|
-
}
|
|
1052
|
-
pcd_pipeline(obj);
|
|
1053
|
-
}
|
|
1054
|
-
});
|
|
1055
|
-
if (obj.cells.categories[obj.use_category_index].hidden_types.length == 0) {
|
|
1056
|
-
select_all_checkbox.property("checked", 1);
|
|
1057
|
-
}
|
|
1058
|
-
top_row.append("span").text("Select All").style("font-size", ".8em").attr("font-family", font);
|
|
1059
|
-
for (const type in data.category2color) {
|
|
1060
|
-
const row = obj.menu_output.append("div").style("margin", "2px");
|
|
1061
|
-
const checkbox = row.append("input").attr("type", "checkbox").property("checked", 1).style("margin-right", "10px").style("vertical-align", "top").style("display", "inline-block").on("change", () => {
|
|
1062
|
-
if (obj.cells.categories[obj.use_category_index].hidden_types.includes(type)) {
|
|
1063
|
-
const index = obj.cells.categories[obj.use_category_index].hidden_types.indexOf(type);
|
|
1064
|
-
if (index !== -1) obj.cells.categories[obj.use_category_index].hidden_types.splice(index, 1);
|
|
1065
|
-
checkbox.property("checked", 1);
|
|
1066
|
-
} else {
|
|
1067
|
-
obj.cells.categories[obj.use_category_index].hidden_types.push(type);
|
|
1068
|
-
}
|
|
1069
|
-
pcd_pipeline(obj);
|
|
1070
|
-
});
|
|
1071
|
-
if (obj.cells.categories[obj.use_category_index].hidden_types.includes(type)) {
|
|
1072
|
-
checkbox.property("checked", 0);
|
|
1073
|
-
}
|
|
1074
|
-
row.append("div").style("display", "inline-block").style("height", "15px").style("width", "15px").style("background-color", data.category2color[type]).style("margin-right", "10px");
|
|
1075
|
-
row.append("span").text(type).attr("font-family", font);
|
|
1076
|
-
row.append("span").html(" n=" + data.categorycount[type]).attr("font-family", font).style("font-size", ".8em").style("float", "right").style("color", "#777");
|
|
1077
|
-
}
|
|
1078
|
-
} else if (data.maxexpvalue) {
|
|
1079
|
-
const scale_height = 30;
|
|
1080
|
-
const scale_width = 150;
|
|
1081
|
-
const scale_div = obj.menu_output.append("div").style("margin", "10px").style("width", "120px").style("height", "100px");
|
|
1082
|
-
scale_div.append("div").text("Gene Expression " + obj.gene_expression.datatype).style("text-align", "center").style("width", "150px").style("margin-bottom", "20px");
|
|
1083
|
-
const svg = scale_div.append("svg").append("g");
|
|
1084
|
-
const colorRange = [obj.gene_expression.color_max, obj.gene_expression.color_min];
|
|
1085
|
-
const colorScale = linear().range(colorRange).domain([data.minexpvalue, data.maxexpvalue]);
|
|
1086
|
-
const defs = svg.append("defs");
|
|
1087
|
-
const linearGradient = defs.append("linearGradient").attr("id", "linear-gradient");
|
|
1088
|
-
linearGradient.append("stop").attr("offset", "0%").attr("stop-color", colorScale(data.maxexpvalue));
|
|
1089
|
-
linearGradient.append("stop").attr("offset", "100%").attr("stop-color", colorScale(data.minexpvalue));
|
|
1090
|
-
svg.append("rect").attr("x", 0).attr("y", 0).attr("width", scale_width).attr("height", scale_height).attr("transform", "translate(12, 0)").style("fill", "url(#linear-gradient)");
|
|
1091
|
-
const y = linear().range([0, scale_width]).domain([data.minexpvalue, data.maxexpvalue]);
|
|
1092
|
-
const legendAxis = axisBottom().scale(y).ticks(5);
|
|
1093
|
-
svg.append("g").attr("class", "legend axis").attr("transform", "translate(12," + scale_height + ")").call(legendAxis);
|
|
1094
|
-
const stats_div = obj.menu_output.append("div").style("padding-bottom", "20px").style("text-align", "center");
|
|
1095
|
-
stats_div.append("p").style("font-size", "13px").style("margin", "2px 0").html("<b>Cells with Expression Data</b> ");
|
|
1096
|
-
stats_div.append("p").style("font-size", "13px").style("margin", "2px 0").html(data.numbercellwithgeneexp + " / " + data.numbercelltotal);
|
|
1097
|
-
const no_exp_div = stats_div.append("div").style("display", "block").style("margin-top", "10px");
|
|
1098
|
-
no_exp_div.append("div").style("display", "inline-block").style("height", "15px").style("width", "15px").style("background-color", obj.gene_expression.color_no_exp ? obj.gene_expression.color_no_exp : "#2C2C2C").style("margin-right", "10px");
|
|
1099
|
-
no_exp_div.append("div").style("display", "inline-block").style("font-size", "13px").html(" Cells without Expression");
|
|
1100
|
-
const boxplot_div = obj.menu_output.append("div");
|
|
1101
|
-
boxplot_div.append("div").style("display", "block").style("padding", "5px").html("Violinplot / Boxplot of </br> Expression by");
|
|
1102
|
-
const boxplot_cat_select = boxplot_div.append("select").style("display", "block");
|
|
1103
|
-
boxplot_cat_select.append("option").attr("value", "none").text("-- Select--");
|
|
1104
|
-
if (obj.cells.categories) {
|
|
1105
|
-
obj.cells.categories.forEach((category, i) => {
|
|
1106
|
-
boxplot_cat_select.append("option").attr("value", category.columnidx).text(category.name);
|
|
1107
|
-
});
|
|
1108
|
-
}
|
|
1109
|
-
boxplot_cat_select.on("change", () => {
|
|
1110
|
-
const gene = obj.gene_expression.genes[obj.use_gene_index];
|
|
1111
|
-
const cat = obj.cells.categories[parseInt(boxplot_cat_select.node().selectedIndex) - 1];
|
|
1112
|
-
const arg = {
|
|
1113
|
-
genome: obj.genome.name,
|
|
1114
|
-
getgeneboxplot: {
|
|
1115
|
-
expfile: obj.gene_expression.file,
|
|
1116
|
-
chr: gene.chr,
|
|
1117
|
-
start: gene.start,
|
|
1118
|
-
stop: gene.stop,
|
|
1119
|
-
genename: gene.gene,
|
|
1120
|
-
cellfile: obj.cells.file,
|
|
1121
|
-
barcodecolumnidx: obj.cells.barcodecolumnidx,
|
|
1122
|
-
categorycolumnidx: parseInt(boxplot_cat_select.node().value),
|
|
1123
|
-
delimiter: obj.cells.delimiter || " ",
|
|
1124
|
-
category_customorder: cat.customorder && cat.values ? true : false,
|
|
1125
|
-
category_autoorder: !cat.customorder ? true : false,
|
|
1126
|
-
cat_values: cat.values,
|
|
1127
|
-
values_count: cat.values_count
|
|
1128
|
-
}
|
|
1129
|
-
};
|
|
1130
|
-
dofetch("singlecell", arg).then((data2) => {
|
|
1131
|
-
if (data2.error) throw data2.error;
|
|
1132
|
-
obj.box_plot = new Menu();
|
|
1133
|
-
make_plot(data2, obj, boxplot_cat_select.node().value);
|
|
1134
|
-
});
|
|
1135
|
-
});
|
|
1136
|
-
}
|
|
1137
|
-
make_zoom_panel(obj);
|
|
1138
|
-
}
|
|
1139
|
-
function make_zoom_panel(obj) {
|
|
1140
|
-
if (obj.show_zoom) {
|
|
1141
|
-
const zoom_div = obj.menu_output.append("div").style("display", "block").text("Zoom").style("margin", "10px 5px 5px 5px").style("padding-top", "10px").style("border-top", "1px solid #929292");
|
|
1142
|
-
const zoom_hide_btn = zoom_div.append("div").style("margin-left", "10px").style("display", "inline-block").style("padding-left", "0px").style("padding-right", "2px").style("float", "right").style("font-size", ".6em").text("MOVE TO CONFIG").on("click", () => {
|
|
1143
|
-
zoom_div.node().remove();
|
|
1144
|
-
obj.show_zoom = false;
|
|
1145
|
-
}).on("mouseover", () => {
|
|
1146
|
-
zoom_hide_btn.style("text-decoration", "underline");
|
|
1147
|
-
}).on("mouseout", () => {
|
|
1148
|
-
zoom_hide_btn.style("text-decoration", "none");
|
|
1149
|
-
});
|
|
1150
|
-
obj.zoom_slider = zoom_div.append("input").style("display", "block").style("padding", "5px").attr("type", "range").attr("min", 1).attr("max", 100).attr("value", obj.camera.fov).style("direction", "rtl").on("change", () => {
|
|
1151
|
-
obj.camera.fov = parseInt(obj.zoom_slider.node().value);
|
|
1152
|
-
obj.camera.updateProjectionMatrix();
|
|
1153
|
-
}).on("mousedown", (event) => {
|
|
1154
|
-
event.stopPropagation();
|
|
1155
|
-
});
|
|
1156
|
-
}
|
|
1157
|
-
}
|
|
1158
|
-
function make_menu(obj) {
|
|
1159
|
-
obj.menu.clear().showunder(obj.menu_button.node());
|
|
1160
|
-
if (obj.cells.categories) {
|
|
1161
|
-
obj.cells.categories.forEach((category, i) => {
|
|
1162
|
-
if (i != obj.use_category_index) {
|
|
1163
|
-
obj.menu.d.append("div").text(category.name).attr("class", "sja_menuoption").on("click", async () => {
|
|
1164
|
-
obj.menu.hide();
|
|
1165
|
-
obj.use_category_index = i;
|
|
1166
|
-
pcd_pipeline(obj);
|
|
1167
|
-
}).append("span").attr("font-family", font).style("display", category.values_count ? "inline-block" : "none").style("font-size", ".8em").style("float", "right").style("color", "#777").style("padding", "3px 5px").html(category.values_count ? " n=" + category.values_count : "");
|
|
1168
|
-
}
|
|
1169
|
-
});
|
|
1170
|
-
}
|
|
1171
|
-
if (obj.gene_expression) {
|
|
1172
|
-
obj.menu.d.append("div").text("Gene expression").attr("class", "sja_menuoption").on("click", () => {
|
|
1173
|
-
obj.menu.clear();
|
|
1174
|
-
const gene_search_div = obj.menu.d.append("div").style("padding", "10px");
|
|
1175
|
-
gene_searchbox({
|
|
1176
|
-
div: gene_search_div.append("div"),
|
|
1177
|
-
resultdiv: gene_search_div.append("div"),
|
|
1178
|
-
genome: obj.genome.name,
|
|
1179
|
-
callback: async (genename) => {
|
|
1180
|
-
const gmlst = await findgenemodel_bysymbol(obj.genome.name, genename);
|
|
1181
|
-
if (gmlst && gmlst[0]) {
|
|
1182
|
-
const gm = gmlst[0];
|
|
1183
|
-
if (!obj.gene_expression.genes) obj.gene_expression.genes = [];
|
|
1184
|
-
const geneidx = obj.gene_expression.genes.findIndex((i) => i.gene == genename);
|
|
1185
|
-
if (geneidx == -1) {
|
|
1186
|
-
obj.gene_expression.genes.push({
|
|
1187
|
-
gene: genename,
|
|
1188
|
-
chr: gm.chr,
|
|
1189
|
-
start: gm.start,
|
|
1190
|
-
stop: gm.stop
|
|
1191
|
-
});
|
|
1192
|
-
obj.use_gene_index = obj.gene_expression.genes.length - 1;
|
|
1193
|
-
} else {
|
|
1194
|
-
obj.use_gene_index = geneidx;
|
|
1195
|
-
}
|
|
1196
|
-
}
|
|
1197
|
-
obj.use_category_index = null;
|
|
1198
|
-
obj.menu.hide();
|
|
1199
|
-
pcd_pipeline(obj);
|
|
1200
|
-
}
|
|
1201
|
-
});
|
|
1202
|
-
});
|
|
1203
|
-
obj.menu.d.append("div").text("Multi-Gene Heatmap").attr("class", "sja_menuoption").on("click", () => {
|
|
1204
|
-
heatmap_menu(obj);
|
|
1205
|
-
});
|
|
1206
|
-
if (obj.gene_expression.genes) {
|
|
1207
|
-
if (obj.gene_expression.genes.length > 1) {
|
|
1208
|
-
obj.menu.d.append("div").style("padding", "5px 10px").text("Previously Selected");
|
|
1209
|
-
}
|
|
1210
|
-
obj.gene_expression.genes.forEach((gene, i) => {
|
|
1211
|
-
if (i != obj.use_gene_index) {
|
|
1212
|
-
obj.menu.d.append("div").text("Gene : " + gene.gene).attr("class", "sja_menuoption").on("click", async () => {
|
|
1213
|
-
obj.menu.hide();
|
|
1214
|
-
obj.use_category_index = null;
|
|
1215
|
-
obj.use_gene_index = i;
|
|
1216
|
-
pcd_pipeline(obj);
|
|
1217
|
-
});
|
|
1218
|
-
}
|
|
1219
|
-
});
|
|
1220
|
-
}
|
|
1221
|
-
}
|
|
1222
|
-
}
|
|
1223
|
-
function make_settings(obj) {
|
|
1224
|
-
obj.settings.clear().showunder(obj.settings_btn.node());
|
|
1225
|
-
const back_color_div = obj.settings.d.append("div").style("display", "block").text("Background Color").style("margin", "5px");
|
|
1226
|
-
const black_div = back_color_div.append("div").style("margin", "5px").style("display", "block");
|
|
1227
|
-
const name = Math.random(), idblack = Math.random(), idwhite = Math.random();
|
|
1228
|
-
const inputblack = black_div.append("input").attr("type", "radio").style("display", "inline-block").attr("name", name).attr("id", idblack).on("change", toggle_background);
|
|
1229
|
-
black_div.append("label").style("display", "inline-block").style("font-size", ".8em").text("Black").style("padding-left", "10px").attr("for", idblack);
|
|
1230
|
-
const white_div = back_color_div.append("div").style("margin", "5px").style("display", "block");
|
|
1231
|
-
const inputwhite = white_div.append("input").attr("type", "radio").style("display", "inline-block").attr("name", name).attr("id", idwhite).on("change", toggle_background);
|
|
1232
|
-
white_div.append("label").style("display", "inline-block").style("font-size", ".8em").text("White").style("padding-left", "10px").attr("for", idwhite);
|
|
1233
|
-
if (obj.use_background_color == 0) {
|
|
1234
|
-
inputwhite.property("checked", 1);
|
|
1235
|
-
} else {
|
|
1236
|
-
inputblack.property("checked", 1);
|
|
1237
|
-
}
|
|
1238
|
-
function toggle_background() {
|
|
1239
|
-
const isblack = obj.background_color == "black";
|
|
1240
|
-
obj.scene.background = new Color(isblack ? 16777215 : 0);
|
|
1241
|
-
obj.use_background_color = isblack ? 0 : 1;
|
|
1242
|
-
obj.background_color = isblack ? "white" : "black";
|
|
1243
|
-
}
|
|
1244
|
-
const point_size_div = obj.settings.d.append("div").style("display", "block").text("Point Size").style("margin", "20px 5px");
|
|
1245
|
-
const point_size_slider = point_size_div.append("input").style("display", "block").style("padding", "5px").attr("type", "range").attr("min", 1).attr("max", 70).attr("value", obj.scene.children[1].material.size * 100).on("change", () => {
|
|
1246
|
-
obj.scene.children[1].material.size = point_size_slider.node().value / 100;
|
|
1247
|
-
});
|
|
1248
|
-
if (obj.show_zoom == false) {
|
|
1249
|
-
const zoom_div = obj.settings.d.append("div").style("display", "block").text("Zoom").style("margin", "20px 5px");
|
|
1250
|
-
const zoom_hide_btn = zoom_div.append("div").style("margin-left", "10px").style("display", "inline-block").style("padding-left", "0px").style("padding-right", "2px").style("float", "right").style("font-size", ".6em").html("MOVE TO </br>LEGEND PANEL").on("click", () => {
|
|
1251
|
-
zoom_div.node().remove();
|
|
1252
|
-
obj.show_zoom = true;
|
|
1253
|
-
make_zoom_panel(obj);
|
|
1254
|
-
}).on("mouseover", () => {
|
|
1255
|
-
zoom_hide_btn.style("text-decoration", "underline");
|
|
1256
|
-
}).on("mouseout", () => {
|
|
1257
|
-
zoom_hide_btn.style("text-decoration", "none");
|
|
1258
|
-
});
|
|
1259
|
-
obj.zoom_slider = zoom_div.append("input").style("display", "block").style("padding", "5px").attr("type", "range").attr("min", 5).attr("max", 70).attr("value", obj.camera.fov).style("direction", "rtl").on("change", () => {
|
|
1260
|
-
obj.camera.fov = parseInt(obj.zoom_slider.node().value);
|
|
1261
|
-
obj.camera.updateProjectionMatrix();
|
|
1262
|
-
});
|
|
1263
|
-
}
|
|
1264
|
-
obj.settings.d.append("div").style("margin", "5px").text("Panning");
|
|
1265
|
-
obj.settings.d.append("div").style("font-size", ".8em").style("text-align", "center").style("margin-bottom", "10px").html('<p style="margin:3px;">Right mouse click </br>+ Mouse move</p>');
|
|
1266
|
-
if (!obj.canvas_2d) {
|
|
1267
|
-
obj.settings.d.append("div").style("margin", "5px").text("Rotate");
|
|
1268
|
-
obj.settings.d.append("div").style("font-size", ".8em").style("text-align", "center").style("margin-bottom", "10px").html('<p style="margin:3px;">Left mouse click </br>+ Mouse move</p>');
|
|
1269
|
-
}
|
|
1270
|
-
obj.settings.d.append("div").attr("class", "sja_menuoption").text("Reset view").style("width", "80px").style("margin", "auto").style("margin-top", "15px").style("margin-bottom", "15px").on("click", () => {
|
|
1271
|
-
inputwhite.property("checked", 1);
|
|
1272
|
-
obj.scene.background = new Color(obj.background_color ? obj.background_color : 16777215);
|
|
1273
|
-
point_size_slider.node().value = obj.point_size ? obj.point_size * 100 : obj.canvas_2d ? 30 : 5;
|
|
1274
|
-
obj.scene.children[1].material.size = obj.point_size ? obj.point_size : obj.canvas_2d ? 0.3 : 0.05;
|
|
1275
|
-
obj.camera.position.z = obj.data_sphere_r * 3;
|
|
1276
|
-
obj.camera.position.x = obj.canvas_2d ? 0 : 20;
|
|
1277
|
-
obj.camera.position.y = obj.canvas_2d ? 0 : -10;
|
|
1278
|
-
const cam_fov_default = 45;
|
|
1279
|
-
obj.camera.fov = parseInt(cam_fov_default);
|
|
1280
|
-
obj.camera.updateProjectionMatrix();
|
|
1281
|
-
obj.zoom_slider.node().value = cam_fov_default;
|
|
1282
|
-
if (obj.canvas_2d) {
|
|
1283
|
-
obj.camera.up.set(0, 1, 0);
|
|
1284
|
-
} else {
|
|
1285
|
-
obj.camera.up.set(0, 0, 1);
|
|
1286
|
-
}
|
|
1287
|
-
obj.controls.target.set(obj.center.x, obj.center.y, obj.center.z);
|
|
1288
|
-
});
|
|
1289
|
-
const screenshot_btn = obj.settings.d.append("div").attr("class", "sja_menuoption").style("padding", "5px").style("width", "80px").style("margin", "auto").style("margin-top", "15px").style("margin-bottom", "15px").html("<b>⧉</b> Capture").on("mousedown", () => {
|
|
1290
|
-
const imgData = obj.renderer.domElement.toDataURL();
|
|
1291
|
-
let imgNode = document.createElement("img");
|
|
1292
|
-
imgNode.src = imgData;
|
|
1293
|
-
screenshot_btn.append("span").style("display", "none").html(
|
|
1294
|
-
'<a download="scRNA_' + (/* @__PURE__ */ new Date()).toLocaleString() + '.png" href="' + imgNode.src + '" title="ImageName">Camera</a>'
|
|
1295
|
-
);
|
|
1296
|
-
}).on("mouseup", () => {
|
|
1297
|
-
screenshot_btn.select("a").node().click();
|
|
1298
|
-
screenshot_btn.selectAll("span").remove();
|
|
1299
|
-
});
|
|
1300
|
-
}
|
|
1301
|
-
function heatmap_menu(obj) {
|
|
1302
|
-
obj.menu.clear();
|
|
1303
|
-
obj.gene_expression.heatmap_genes = [];
|
|
1304
|
-
obj.use_heatmap_category_index = null;
|
|
1305
|
-
const heatmap_menu_div = obj.menu.d.append("div").style("display", "block").style("padding", "10px");
|
|
1306
|
-
const genes_div = heatmap_menu_div.append("div").style("display", "block");
|
|
1307
|
-
const gene_search_div = genes_div.append("div").style("display", "inline-block").style("vertical-align", "top").style("padding", "10px");
|
|
1308
|
-
gene_search_div.append("div").style("display", "block").style("padding-bottom", "5px").text("Add Genes");
|
|
1309
|
-
gene_search_div.append("textarea").attr("rows", "4").attr("cols", "20").attr("placeholder", "Type gene names seperated by space");
|
|
1310
|
-
const catagory_div = heatmap_menu_div.append("div");
|
|
1311
|
-
catagory_div.append("div").style("display", "block").style("padding-bottom", "5px").style("padding-left", "10px").text("Heatmap by");
|
|
1312
|
-
const cat_select = catagory_div.append("select").style("display", "block").style("margin-left", "10px");
|
|
1313
|
-
cat_select.append("option").attr("value", "none").text("-- Select--");
|
|
1314
|
-
if (obj.cells.categories) {
|
|
1315
|
-
obj.cells.categories.forEach((category, i) => {
|
|
1316
|
-
cat_select.append("option").attr("value", category.columnidx).text(category.name);
|
|
1317
|
-
});
|
|
1318
|
-
}
|
|
1319
|
-
cat_select.on("change", () => {
|
|
1320
|
-
obj.use_heatmap_category_index = parseInt(cat_select.node().value);
|
|
1321
|
-
});
|
|
1322
|
-
heatmap_menu_div.append("button").text("Heatmap").style("display", "block").style("float", "right").style("margin", "5px").on("click", async () => {
|
|
1323
|
-
const input_genelist = gene_search_div.select("textarea").node().value;
|
|
1324
|
-
const genelist = input_genelist.split(" ");
|
|
1325
|
-
for (const gene of genelist) {
|
|
1326
|
-
const gmlst = await findgenemodel_bysymbol(obj.genome.name, gene);
|
|
1327
|
-
if (gmlst && gmlst[0]) {
|
|
1328
|
-
const gm = gmlst[0];
|
|
1329
|
-
if (!obj.gene_expression.heatmap_genes) obj.gene_expression.heatmap_genes = [];
|
|
1330
|
-
const geneidx = obj.gene_expression.heatmap_genes.findIndex((i) => i.gene == gene);
|
|
1331
|
-
if (geneidx == -1) {
|
|
1332
|
-
obj.gene_expression.heatmap_genes.push({
|
|
1333
|
-
gene,
|
|
1334
|
-
chr: gm.chr,
|
|
1335
|
-
start: gm.start,
|
|
1336
|
-
stop: gm.stop
|
|
1337
|
-
});
|
|
1338
|
-
}
|
|
1339
|
-
}
|
|
1340
|
-
}
|
|
1341
|
-
const arg = {
|
|
1342
|
-
genome: obj.genome.name,
|
|
1343
|
-
getheatmap: {
|
|
1344
|
-
expfile: obj.gene_expression.file,
|
|
1345
|
-
gene_list: obj.gene_expression.heatmap_genes,
|
|
1346
|
-
cellfile: obj.cells.file,
|
|
1347
|
-
barcodecolumnidx: obj.cells.barcodecolumnidx,
|
|
1348
|
-
categorycolumnidx: parseInt(cat_select.node().value),
|
|
1349
|
-
delimiter: obj.cells.delimiter || " "
|
|
1350
|
-
}
|
|
1351
|
-
};
|
|
1352
|
-
dofetch("singlecell", arg).then((data) => {
|
|
1353
|
-
if (data.error) throw data.error;
|
|
1354
|
-
obj.menu.hide();
|
|
1355
|
-
make_heatmap(data, obj, cat_select.node().value);
|
|
1356
|
-
});
|
|
1357
|
-
});
|
|
1358
|
-
}
|
|
1359
|
-
function make_plot(data, obj, colidx) {
|
|
1360
|
-
const gene = obj.gene_expression.genes[obj.use_gene_index];
|
|
1361
|
-
const pane = newpane({ x: 600, y: 400 });
|
|
1362
|
-
const cat = obj.cells.categories.find((x) => x.columnidx == colidx);
|
|
1363
|
-
pane.header.text("Violinplot/Boxplot for " + gene.gene + " Expression by " + cat.name);
|
|
1364
|
-
const control_panel = pane.pane.append("div").style("margin", "10px 10px 10px 15px");
|
|
1365
|
-
const svg = pane.pane.append("svg").style("margin", "10px");
|
|
1366
|
-
const plot_select = control_panel.append("select").style("display", "inline-block");
|
|
1367
|
-
plot_select.append("option").attr("value", "violin").text("Violin Plot");
|
|
1368
|
-
plot_select.append("option").attr("value", "box").text("Box Plot");
|
|
1369
|
-
plot_select.on("change", () => {
|
|
1370
|
-
apply();
|
|
1371
|
-
});
|
|
1372
|
-
const cell_select_div = control_panel.append("div").style("display", "inline-block").style("padding-left", "15px").text("Cells without expression");
|
|
1373
|
-
const cell_select = cell_select_div.append("select").style("display", "inline-block").style("margin-left", "5px");
|
|
1374
|
-
cell_select.append("option").attr("value", "include").text("Include");
|
|
1375
|
-
cell_select.append("option").attr("value", "exclude").text("Exclude");
|
|
1376
|
-
cell_select.on("change", () => {
|
|
1377
|
-
apply();
|
|
1378
|
-
});
|
|
1379
|
-
make_violin_plot(data, svg);
|
|
1380
|
-
function apply() {
|
|
1381
|
-
const gene2 = obj.gene_expression.genes[obj.use_gene_index];
|
|
1382
|
-
const arg = {
|
|
1383
|
-
genome: obj.genome.name,
|
|
1384
|
-
getgeneboxplot: {
|
|
1385
|
-
expfile: obj.gene_expression.file,
|
|
1386
|
-
chr: gene2.chr,
|
|
1387
|
-
start: gene2.start,
|
|
1388
|
-
stop: gene2.stop,
|
|
1389
|
-
genename: gene2.gene,
|
|
1390
|
-
cellfile: obj.cells.file,
|
|
1391
|
-
barcodecolumnidx: obj.cells.barcodecolumnidx,
|
|
1392
|
-
categorycolumnidx: parseInt(colidx),
|
|
1393
|
-
delimiter: obj.cells.delimiter || " ",
|
|
1394
|
-
category_customorder: cat.customorder && cat.values ? true : false,
|
|
1395
|
-
category_autoorder: !cat.customorder ? true : false,
|
|
1396
|
-
cat_values: cat.values,
|
|
1397
|
-
values_count: cat.values_count
|
|
1398
|
-
}
|
|
1399
|
-
};
|
|
1400
|
-
if (cell_select.node().value == "exclude") {
|
|
1401
|
-
arg.getgeneboxplot.exclude_cells = true;
|
|
1402
|
-
}
|
|
1403
|
-
dofetch("singlecell", arg).then((data2) => {
|
|
1404
|
-
if (data2.error) throw data2.error;
|
|
1405
|
-
if (plot_select.node().value == "box") make_box_plot(data2, svg);
|
|
1406
|
-
else if (plot_select.node().value == "violin") make_violin_plot(data2, svg);
|
|
1407
|
-
});
|
|
1408
|
-
}
|
|
1409
|
-
}
|
|
1410
|
-
function make_violin_plot(data, svg) {
|
|
1411
|
-
svg.selectAll("*").remove();
|
|
1412
|
-
let box_height = 50, box_width = 200, barspace = 2, axis_height = 30;
|
|
1413
|
-
const label_width = get_max_labelwidth(data.boxplots, svg);
|
|
1414
|
-
const x_scale = linear().range([0, box_width]).domain([data.minexpvalue, data.maxexpvalue]);
|
|
1415
|
-
const y_scale = linear().range([box_height, 0]).domain([0, 1]);
|
|
1416
|
-
const svg_height = data.boxplots.length * (box_height + barspace) + axis_height;
|
|
1417
|
-
const svg_width = box_width + label_width + 20;
|
|
1418
|
-
svg.transition().attr("width", svg_width).attr("height", svg_height);
|
|
1419
|
-
if (data.boxplots) {
|
|
1420
|
-
data.boxplots.forEach((boxplot, i) => {
|
|
1421
|
-
const g = svg.append("g").attr("transform", "translate(" + label_width + "," + (i * (box_height + barspace) + axis_height) + ")");
|
|
1422
|
-
const xlabel = g.append("text").text(boxplot.category + " (" + boxplot.numberofcells + ")").attr("transform", "translate(-4," + box_height / 2 + ")").attr("text-anchor", "end").attr("font-size", 15).attr("font-family", font).attr("dominant-baseline", "central");
|
|
1423
|
-
if (boxplot.density) {
|
|
1424
|
-
const density_max = Math.max(...boxplot.density);
|
|
1425
|
-
const line = line_default().x(function(d, j) {
|
|
1426
|
-
return x_scale(j * data.maxexpvalue / boxplot.density.length);
|
|
1427
|
-
}).y(function(d) {
|
|
1428
|
-
return y_scale(d / density_max) / 2;
|
|
1429
|
-
}).curve(monotoneX);
|
|
1430
|
-
const area = area_default().x(function(d, j) {
|
|
1431
|
-
return x_scale(j * data.maxexpvalue / boxplot.density.length);
|
|
1432
|
-
}).y0(function(d) {
|
|
1433
|
-
const temp = y_scale(d / density_max) / 2;
|
|
1434
|
-
return box_height - temp;
|
|
1435
|
-
}).y1(function(d) {
|
|
1436
|
-
return y_scale(d / density_max) / 2;
|
|
1437
|
-
}).curve(monotoneX);
|
|
1438
|
-
g.append("path").datum(boxplot.density).attr("class", "area").attr("d", area).style("fill", boxplot.color).style("stroke", "black").style("stroke-width", 0.5);
|
|
1439
|
-
}
|
|
1440
|
-
});
|
|
1441
|
-
const legendAxis = axisTop().scale(x_scale).ticks(5);
|
|
1442
|
-
svg.append("g").attr("class", "legend axis").attr("transform", "translate(" + label_width + "," + (axis_height - 10) + ")").call(legendAxis);
|
|
1443
|
-
}
|
|
1444
|
-
}
|
|
1445
|
-
function make_box_plot(data, svg) {
|
|
1446
|
-
svg.selectAll("*").remove();
|
|
1447
|
-
let box_height = 36, box_width = 200, barspace = 16, axis_height = 30;
|
|
1448
|
-
const label_width = get_max_labelwidth(data.boxplots, svg);
|
|
1449
|
-
const x_scale = linear().range([0, box_width]).domain([data.minexpvalue, data.maxexpvalue]);
|
|
1450
|
-
const y_scale = linear().range([box_height, 0]).domain([0, 1]);
|
|
1451
|
-
const svg_height = data.boxplots.length * (box_height + barspace) + axis_height;
|
|
1452
|
-
const svg_width = box_width + label_width + 20;
|
|
1453
|
-
svg.transition().attr("width", svg_width).attr("height", svg_height);
|
|
1454
|
-
if (data.boxplots) {
|
|
1455
|
-
data.boxplots.forEach((boxplot, i) => {
|
|
1456
|
-
const g = svg.append("g").attr("transform", "translate(" + label_width + "," + (i * (box_height + barspace) + axis_height) + ")");
|
|
1457
|
-
const xlabel = g.append("text").text(boxplot.category + " (" + boxplot.numberofcells + ")").attr("transform", "translate(-4," + box_height / 2 + ")").attr("text-anchor", "end").attr("font-size", 15).attr("font-family", font).attr("dominant-baseline", "central");
|
|
1458
|
-
if (boxplot.p75) {
|
|
1459
|
-
g.append("line").attr("x1", x_scale(boxplot.w1)).attr("y1", box_height / 2).attr("x2", x_scale(boxplot.w2)).attr("y2", box_height / 2).attr("stroke-width", 2).attr("stroke", "black");
|
|
1460
|
-
g.append("rect").attr("x", x_scale(boxplot.p25)).attr("y", 0).attr("width", x_scale(boxplot.p75 - boxplot.p25)).attr("height", box_height).attr("fill", boxplot.color);
|
|
1461
|
-
g.append("line").attr("x1", x_scale(boxplot.w1)).attr("y1", 0).attr("x2", x_scale(boxplot.w1)).attr("y2", box_height).attr("stroke-width", 2).attr("stroke", "black");
|
|
1462
|
-
g.append("line").attr("x1", x_scale(boxplot.p50)).attr("y1", 0).attr("x2", x_scale(boxplot.p50)).attr("y2", box_height).attr("stroke-width", 2).attr("stroke", "white");
|
|
1463
|
-
g.append("line").attr("x1", x_scale(boxplot.w2)).attr("y1", 0).attr("x2", x_scale(boxplot.w2)).attr("y2", box_height).attr("stroke-width", 2).attr("stroke", "black");
|
|
1464
|
-
if (boxplot.out) {
|
|
1465
|
-
for (const outlier of boxplot.out) {
|
|
1466
|
-
g.append("circle").attr("cx", x_scale(outlier.value)).attr("cy", box_height / 2).attr("r", 2).attr("fill", "#901739");
|
|
1467
|
-
}
|
|
1468
|
-
}
|
|
1469
|
-
}
|
|
1470
|
-
});
|
|
1471
|
-
const legendAxis = axisTop().scale(x_scale).ticks(5);
|
|
1472
|
-
svg.append("g").attr("class", "legend axis").attr("transform", "translate(" + label_width + "," + (axis_height - 10) + ")").call(legendAxis);
|
|
1473
|
-
}
|
|
1474
|
-
}
|
|
1475
|
-
function make_heatmap(data, obj, colidx) {
|
|
1476
|
-
const pane = newpane({ x: 600, y: 400 });
|
|
1477
|
-
const cat = obj.cells.categories.find((x) => x.columnidx == colidx);
|
|
1478
|
-
pane.header.text("Heatmap for Gene Expression by " + cat.name);
|
|
1479
|
-
const svg = pane.pane.append("svg").style("margin", "10px");
|
|
1480
|
-
let gene_list = [];
|
|
1481
|
-
for (const gene of data.gene_heatmap) gene_list.push(gene.genename);
|
|
1482
|
-
let means = [];
|
|
1483
|
-
data.gene_heatmap.forEach((gene, i) => {
|
|
1484
|
-
data.gene_heatmap[i].heatmap.forEach((category) => {
|
|
1485
|
-
means.push(category.mean);
|
|
1486
|
-
});
|
|
1487
|
-
});
|
|
1488
|
-
const max_mean = Math.max(...means);
|
|
1489
|
-
let categories = [];
|
|
1490
|
-
for (const category of data.gene_heatmap[0].heatmap)
|
|
1491
|
-
categories.push(category.category + " (" + category.numberofcells + ")");
|
|
1492
|
-
let box_height = 20, box_width = 80, barspace = 2, gene_lable_height = 30, legend_width = 60;
|
|
1493
|
-
const label_width = get_max_labelwidth(data.gene_heatmap[0].heatmap, svg);
|
|
1494
|
-
const svg_height = (box_height + barspace) * categories.length + gene_lable_height;
|
|
1495
|
-
const svg_width = (box_width + barspace) * gene_list.length + label_width + legend_width + 20;
|
|
1496
|
-
svg.transition().attr("width", svg_width).attr("height", svg_height);
|
|
1497
|
-
const x_scale = band().range([0, (box_width + barspace) * gene_list.length]).domain(gene_list).padding(0.05);
|
|
1498
|
-
svg.append("g").style("font-size", 15).attr("transform", "translate(" + label_width + ",0)").call(axisBottom(x_scale).tickSize(0)).select(".domain").remove();
|
|
1499
|
-
const y_scale = band().range([(box_height + barspace) * categories.length, 0]).domain(categories).padding(0.05);
|
|
1500
|
-
svg.append("g").style("font-size", 15).attr("transform", "translate(" + label_width + "," + gene_lable_height + ")").call(axisLeft(y_scale).tickSize(0)).select(".domain").remove();
|
|
1501
|
-
var myColor = sequential().interpolator(plasma).domain([0, max_mean]);
|
|
1502
|
-
const div = pane.pane.append("div").style("position", "absolute").attr("class", "tooltip").style("background-color", "white").style("border", "solid").style("border-width", "2px").style("border-radius", "5px").style("padding", "5px").style("opacity", 0);
|
|
1503
|
-
data.gene_heatmap.forEach((gene, i) => {
|
|
1504
|
-
data.gene_heatmap[i].heatmap.forEach((category, j) => {
|
|
1505
|
-
const g = svg.append("g").attr("transform", "translate(" + label_width + "," + gene_lable_height + ")");
|
|
1506
|
-
g.append("rect").attr("x", x_scale(gene.genename)).attr("y", y_scale(category.category + " (" + category.numberofcells + ")")).attr("width", x_scale.bandwidth()).attr("height", y_scale.bandwidth()).style("fill", myColor(category.mean)).style("stroke-width", 4).style("stroke", "none").style("opacity", 0.8).on("mouseover", function(event) {
|
|
1507
|
-
div.transition().duration(200).style("opacity", 0.9);
|
|
1508
|
-
div.html("Mean Expression: " + category.mean).style("left", pointer_default(event, this)[0] + 70 + "px").style("top", pointer_default(event, this)[1] + 20 + "px");
|
|
1509
|
-
}).on("mouseout", function() {
|
|
1510
|
-
div.transition().duration(500).style("opacity", 0);
|
|
1511
|
-
});
|
|
1512
|
-
});
|
|
1513
|
-
});
|
|
1514
|
-
const legend_data = myColor.ticks(10).reverse();
|
|
1515
|
-
legend_data.unshift(max_mean.toFixed(2));
|
|
1516
|
-
const legend = svg.selectAll(".legend").data(legend_data).enter().append("g").attr("class", "legend").attr("transform", function(d, i) {
|
|
1517
|
-
return "translate(" + (svg_width - legend_width) + "," + (30 + i * 20) + ")";
|
|
1518
|
-
});
|
|
1519
|
-
legend.append("rect").attr("width", 20).attr("height", 20).style("fill", myColor).style("opacity", 0.8);
|
|
1520
|
-
legend.append("text").attr("x", 26).attr("y", 10).attr("dy", ".35em").text(String);
|
|
1521
|
-
}
|
|
1522
|
-
function get_max_labelwidth(items, svg) {
|
|
1523
|
-
let textwidth = 0;
|
|
1524
|
-
for (const i of items) {
|
|
1525
|
-
svg.append("text").text(i.category + " (" + i.numberofcells + ")").attr("font-family", font).attr("font-size", 15).each(function() {
|
|
1526
|
-
textwidth = Math.max(textwidth, this.getBBox().width);
|
|
1527
|
-
}).remove();
|
|
1528
|
-
}
|
|
1529
|
-
return textwidth + 4;
|
|
1530
|
-
}
|
|
1531
|
-
async function make_legend(arg, obj) {
|
|
1532
|
-
if (!arg.legendimg) return;
|
|
1533
|
-
const img_div = obj.holder.append("div").style("margin-top", "5px");
|
|
1534
|
-
obj.legendimg = arg.legendimg;
|
|
1535
|
-
obj.legend = {
|
|
1536
|
-
holder: img_div,
|
|
1537
|
-
legendcolor: "#7D6836"
|
|
1538
|
-
};
|
|
1539
|
-
let shown = !arg.foldlegend;
|
|
1540
|
-
img_div.append("div").text("LEGEND").attr("class", "sja_clb").style("display", "inline-block").style("font-size", ".7em").style("color", obj.legend.legendcolor).style("font-family", font).on("click", () => {
|
|
1541
|
-
if (shown) {
|
|
1542
|
-
shown = false;
|
|
1543
|
-
disappear(div2);
|
|
1544
|
-
} else {
|
|
1545
|
-
shown = true;
|
|
1546
|
-
appear(div2);
|
|
1547
|
-
}
|
|
1548
|
-
});
|
|
1549
|
-
const div2 = obj.holder.append("div").style("border-top", "solid 1px " + obj.legend.legendcolor).style("background-color", "#FCFBF7");
|
|
1550
|
-
obj.legend.holder = div2.append("table").style("border-spacing", "15px").style("border-collapse", "separate");
|
|
1551
|
-
const [tr, td] = legend_newrow(obj, obj.legendimg.name || "");
|
|
1552
|
-
const data = await dofetch2("img?file=" + obj.legendimg.file);
|
|
1553
|
-
if (data.error) {
|
|
1554
|
-
td.text(data.error);
|
|
1555
|
-
return;
|
|
1556
|
-
}
|
|
1557
|
-
let fold = true;
|
|
1558
|
-
const img = td.append("img").attr("class", "sja_clbb").attr("src", data.src).style("height", "80px");
|
|
1559
|
-
img.on("click", () => {
|
|
1560
|
-
if (fold) {
|
|
1561
|
-
fold = false;
|
|
1562
|
-
img.transition().style("height", obj.legendimg.height ? obj.legendimg.height + "px" : "auto");
|
|
1563
|
-
} else {
|
|
1564
|
-
fold = true;
|
|
1565
|
-
img.transition().style("height", "80px");
|
|
1566
|
-
}
|
|
1567
|
-
});
|
|
1568
|
-
}
|
|
1569
|
-
export {
|
|
1570
|
-
init
|
|
1571
|
-
};
|
|
1572
|
-
//# sourceMappingURL=singlecell-RO3BL5OO.js.map
|