@sjcrh/proteinpaint-client 2.193.0 → 2.195.0

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.
Files changed (916) hide show
  1. package/dist/2dmaf-GTD3AXGT.js +1373 -0
  2. package/dist/AIProjectAdmin-ALMSVHFX.js +958 -0
  3. package/dist/AppHeader-RK2YRITI.js +835 -0
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  7. package/dist/DEinput-I62VHD2U.js +301 -0
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  15. package/dist/GeneExpInput-EHWHQTRV.js +367 -0
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  172. package/dist/dnaMethylation-XNRJIBAH.js +38 -0
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  847. /package/dist/{plot.wsi-MR6JMOXW.js.map → plot.wsi-YMDUOZ57.js.map} +0 -0
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  849. /package/dist/{profileForms-XXGJVF2T.js.map → profileForms-TCPZPI22.js.map} +0 -0
  850. /package/dist/{profilePlot-J2C35OEY.js.map → profilePlot-4RKKICKC.js.map} +0 -0
  851. /package/dist/{qualitative-N7S2JHZM.js.map → qualitative-NCFIVW6S.js.map} +0 -0
  852. /package/dist/{radar2-CDDOQGQX.js.map → radar2-UJFFZE7T.js.map} +0 -0
  853. /package/dist/{radarFacility2-ZQTHO2ON.js.map → radarFacility2-ATQBCF3N.js.map} +0 -0
  854. /package/dist/{regression-PBGAMZAV.js.map → regression-4RSS7447.js.map} +0 -0
  855. /package/dist/{regression.inputs-54E5YKI4.js.map → regression.inputs-5XGUGNWV.js.map} +0 -0
  856. /package/dist/{regression.inputs.term-52MBTMVM.js.map → regression.inputs.term-LSJAZWE4.js.map} +0 -0
  857. /package/dist/{regression.inputs.values.table-F3FOAYFV.js.map → regression.inputs.values.table-GNIJZETG.js.map} +0 -0
  858. /package/dist/{regression.integration.spec-M4RPJUE4.js.map → regression.integration.spec-MV652K47.js.map} +0 -0
  859. /package/dist/{regression.results-JOK6I2ZD.js.map → regression.results-M3YH6ZD3.js.map} +0 -0
  860. /package/dist/{regression.spec-O4HZB2HQ.js.map → regression.spec-455WPZHP.js.map} +0 -0
  861. /package/dist/{report-BDDTM7SV.js.map → report-MH3V7SHZ.js.map} +0 -0
  862. /package/dist/{sampleScatter.spec-272GLYEK.js.map → sampleScatter.spec-OTIL3JDG.js.map} +0 -0
  863. /package/dist/{sampleView-E6OHEEP4.js.map → sampleView-DHACOCEG.js.map} +0 -0
  864. /package/dist/{samplelst-3LNF3DBG.js.map → samplelst-F3AXOE2D.js.map} +0 -0
  865. /package/dist/{samplematrix-HL445X7I.js.map → samplematrix-M6CKKVNE.js.map} +0 -0
  866. /package/dist/{sc-4LELHVIS.js.map → sc-S5XA37JJ.js.map} +0 -0
  867. /package/dist/{scatter-IZIZURQD.js.map → scatter-IRPFNDHW.js.map} +0 -0
  868. /package/dist/{scatter.integration.spec-BBEWMA7M.js.map → scatter.integration.spec-5FWVHMVJ.js.map} +0 -0
  869. /package/dist/{selectGenomeWithTklst-5LQGT4Z7.js.map → selectGenomeWithTklst-NIOUX6MV.js.map} +0 -0
  870. /package/dist/{singleCellCellType-T3ZT64EK.js.map → singleCellCellType-FTGLNH2J.js.map} +0 -0
  871. /package/dist/{singleCellCellType.unit.spec-AE4IAHOF.js.map → singleCellCellType.unit.spec-BJ5YZAXF.js.map} +0 -0
  872. /package/dist/{singleCellGeneExpression-SRJXSDEB.js.map → singleCellGeneExpression-56EDDG5H.js.map} +0 -0
  873. /package/dist/{singleCellGeneExpression.unit.spec-EPL73UUO.js.map → singleCellGeneExpression.unit.spec-XSQRWAI3.js.map} +0 -0
  874. /package/dist/{singleCellPlot-P2BHFTYZ.js.map → singleCellPlot-TH77EJZ4.js.map} +0 -0
  875. /package/dist/{singlecell-7KRD5DP7.js.map → singlecell-3QZQZM32.js.map} +0 -0
  876. /package/dist/{singlecell-32SSD7VN.js.map → singlecell-7KJMBASC.js.map} +0 -0
  877. /package/dist/{snp-LE5R377N.js.map → snp-YXG5O4U4.js.map} +0 -0
  878. /package/dist/{snp.unit.spec-UY6KQ5NJ.js.map → snp.unit.spec-O27J7OOK.js.map} +0 -0
  879. /package/dist/{snplocus-CP34ABUJ.js.map → snplocus-CQZSC7P6.js.map} +0 -0
  880. /package/dist/{spliceevent.a53ss.diagram-JWLWQDNJ.js.map → spliceevent.a53ss.diagram-K5ZDPZE6.js.map} +0 -0
  881. /package/dist/{spliceevent.exonskip.diagram-C5526P7P.js.map → spliceevent.exonskip.diagram-A2VZ3TTF.js.map} +0 -0
  882. /package/dist/{spliceevent.noeventdiagram-352M63YB.js.map → spliceevent.noeventdiagram-DJDA6ENK.js.map} +0 -0
  883. /package/dist/{ssGSEA-BFTCECV3.js.map → ssGSEA-3FTGRUTC.js.map} +0 -0
  884. /package/dist/{ssGSEA.unit.spec-4OUCKRDQ.js.map → ssGSEA.unit.spec-GF35KBTX.js.map} +0 -0
  885. /package/dist/{summarizeCnvGeneexp-Y3AWFIZA.js.map → summarizeCnvGeneexp-6IDTNOYE.js.map} +0 -0
  886. /package/dist/{summarizeMutationCnv-KCOVQEBC.js.map → summarizeMutationCnv-BMEN3XNV.js.map} +0 -0
  887. /package/dist/{summarizeMutationDiagnosis-EQXEQABW.js.map → summarizeMutationDiagnosis-LW6K6373.js.map} +0 -0
  888. /package/dist/{summarizeMutationSurvival-4VGLG4SC.js.map → summarizeMutationSurvival-E7REF2VY.js.map} +0 -0
  889. /package/dist/{summary-DXYCBNI4.js.map → summary-MKA7OJKE.js.map} +0 -0
  890. /package/dist/{summary.integration.spec-MZTJISLP.js.map → summary.integration.spec-IV6I6SNJ.js.map} +0 -0
  891. /package/dist/{summaryInput-5Z3XVIL6.js.map → summaryInput-NET6SPM4.js.map} +0 -0
  892. /package/dist/{sunburst-WVSQJYP2.js.map → sunburst-CO3MXFTJ.js.map} +0 -0
  893. /package/dist/{survival-3R3J2JBE.js.map → survival-MIPCEBS3.js.map} +0 -0
  894. /package/dist/{survival-XQWFVGCJ.js.map → survival-QQXTCNDU.js.map} +0 -0
  895. /package/dist/{svg2pdf.es.min-H4DXBG4O.js.map → svg2pdf.es.min-P2F6SSVJ.js.map} +0 -0
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  897. /package/dist/{svmr-TIIMFKG7.js.map → svmr-J2JLQGEE.js.map} +0 -0
  898. /package/dist/{table-5RFTXIQL.js.map → table-7YL7I4GH.js.map} +0 -0
  899. /package/dist/{termCollection-23QXTZDN.js.map → termCollection-LNEN72IV.js.map} +0 -0
  900. /package/dist/{termCollection-7KXABWVW.js.map → termCollection-SOLNYAZ4.js.map} +0 -0
  901. /package/dist/{termCollection.unit.spec-4AN2Z4PQ.js.map → termCollection.unit.spec-LTX7UVYP.js.map} +0 -0
  902. /package/dist/{tk-WW6PJGPQ.js.map → tk-RZDP2YT5.js.map} +0 -0
  903. /package/dist/{tp.ui-S5PO3MPH.js.map → tp.ui-T6XXBHHD.js.map} +0 -0
  904. /package/dist/{tvs.dt-O7LUM5TK.js.map → tvs.dt-7APM37Y3.js.map} +0 -0
  905. /package/dist/{tvs.dtcnv.categorical-2OUFOD3W.js.map → tvs.dtcnv.categorical-YIPXQSIL.js.map} +0 -0
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  907. /package/dist/{tvs.dtfusion-KXQMP3UF.js.map → tvs.dtfusion-2JIIPDTN.js.map} +0 -0
  908. /package/dist/{tvs.dtsnvindel-PWHFTWZU.js.map → tvs.dtsnvindel-HO2PUFN2.js.map} +0 -0
  909. /package/dist/{tvs.dtsv-25FLS572.js.map → tvs.dtsv-7KCWSUYO.js.map} +0 -0
  910. /package/dist/{tvs.samplelst-FLXNJFIV.js.map → tvs.samplelst-KKWJQNLW.js.map} +0 -0
  911. /package/dist/{tvs.termCollection-PSVOMJE4.js.map → tvs.termCollection-R2IGRG2U.js.map} +0 -0
  912. /package/dist/{violin-SWMEFWRA.js.map → violin-OTPZQTGA.js.map} +0 -0
  913. /package/dist/{violin.integration.spec-6EQ6GC2N.js.map → violin.integration.spec-KESWDSBM.js.map} +0 -0
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  916. /package/dist/{vocabulary-WLHYHDX7.js.map → vocabulary-XXDHHHPJ.js.map} +0 -0
@@ -1,1572 +0,0 @@
1
- import {
2
- BufferGeometry,
3
- Color,
4
- EventDispatcher,
5
- FileLoader,
6
- Float32BufferAttribute,
7
- Int32BufferAttribute,
8
- LinearSRGBColorSpace,
9
- Loader,
10
- MOUSE,
11
- MathUtils,
12
- NoToneMapping,
13
- PerspectiveCamera,
14
- Points,
15
- PointsMaterial,
16
- Quaternion,
17
- Scene,
18
- Vector2,
19
- Vector3,
20
- WebGLRenderer
21
- } from "./chunk-72PLI3GC.js";
22
- import {
23
- legend_newrow
24
- } from "./chunk-SC6IPDJR.js";
25
- import {
26
- schemeCategory20
27
- } from "./chunk-V2OJLJSK.js";
28
- import {
29
- findgenemodel_bysymbol,
30
- gene_searchbox
31
- } from "./chunk-OR43PGBV.js";
32
- import "./chunk-NLQQIVTC.js";
33
- import {
34
- appear2 as appear,
35
- disappear2 as disappear,
36
- font,
37
- newpane,
38
- sayerror
39
- } from "./chunk-L7VDSIM7.js";
40
- import "./chunk-HJ6L54YS.js";
41
- import "./chunk-LSEFWW72.js";
42
- import "./chunk-UXDVUCXU.js";
43
- import {
44
- Menu
45
- } from "./chunk-HYOEWQ5P.js";
46
- import "./chunk-HBW42TDT.js";
47
- import "./chunk-LQJMCE7G.js";
48
- import "./chunk-FN5XPUPH.js";
49
- import "./chunk-IIT367QZ.js";
50
- import "./chunk-RZGEKL77.js";
51
- import "./chunk-KM4JBR26.js";
52
- import "./chunk-COYULNJF.js";
53
- import {
54
- dofetch,
55
- dofetch2
56
- } from "./chunk-6G4YOMWW.js";
57
- import "./chunk-7IYJZZQI.js";
58
- import "./chunk-M3J4MINX.js";
59
- import "./chunk-PF4DSFDR.js";
60
- import "./chunk-I73KUUYG.js";
61
- import "./chunk-IVXCWCKS.js";
62
- import "./chunk-7KRS7L4U.js";
63
- import "./chunk-BKPDYW5T.js";
64
- import "./chunk-JNITUVXP.js";
65
- import {
66
- area_default,
67
- line_default,
68
- monotoneX,
69
- plasma
70
- } from "./chunk-TJYRBEBK.js";
71
- import {
72
- axisBottom,
73
- axisLeft,
74
- axisTop
75
- } from "./chunk-LOZEKOES.js";
76
- import "./chunk-VQZ2Z5YU.js";
77
- import {
78
- band,
79
- linear,
80
- ordinal,
81
- sequential
82
- } from "./chunk-SOTB4FRE.js";
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- import "./chunk-TLT4YIG3.js";
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- import "./chunk-KYBIQBXE.js";
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- import {
86
- pointer_default
87
- } from "./chunk-I6Y4O3RR.js";
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- import "./chunk-OMR2DT66.js";
89
- import "./chunk-DQC5FFGV.js";
90
- import "./chunk-HFNDKYVF.js";
91
-
92
- // ../node_modules/three/examples/jsm/loaders/PCDLoader.js
93
- var PCDLoader = class extends Loader {
94
- constructor(manager) {
95
- super(manager);
96
- this.littleEndian = true;
97
- }
98
- load(url, onLoad, onProgress, onError) {
99
- const scope = this;
100
- const loader = new FileLoader(scope.manager);
101
- loader.setPath(scope.path);
102
- loader.setResponseType("arraybuffer");
103
- loader.setRequestHeader(scope.requestHeader);
104
- loader.setWithCredentials(scope.withCredentials);
105
- loader.load(url, function(data) {
106
- try {
107
- onLoad(scope.parse(data));
108
- } catch (e) {
109
- if (onError) {
110
- onError(e);
111
- } else {
112
- console.error(e);
113
- }
114
- scope.manager.itemError(url);
115
- }
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- }, onProgress, onError);
117
- }
118
- parse(data) {
119
- function decompressLZF(inData, outLength) {
120
- const inLength = inData.length;
121
- const outData = new Uint8Array(outLength);
122
- let inPtr = 0;
123
- let outPtr = 0;
124
- let ctrl;
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- let len;
126
- let ref;
127
- do {
128
- ctrl = inData[inPtr++];
129
- if (ctrl < 1 << 5) {
130
- ctrl++;
131
- if (outPtr + ctrl > outLength) throw new Error("Output buffer is not large enough");
132
- if (inPtr + ctrl > inLength) throw new Error("Invalid compressed data");
133
- do {
134
- outData[outPtr++] = inData[inPtr++];
135
- } while (--ctrl);
136
- } else {
137
- len = ctrl >> 5;
138
- ref = outPtr - ((ctrl & 31) << 8) - 1;
139
- if (inPtr >= inLength) throw new Error("Invalid compressed data");
140
- if (len === 7) {
141
- len += inData[inPtr++];
142
- if (inPtr >= inLength) throw new Error("Invalid compressed data");
143
- }
144
- ref -= inData[inPtr++];
145
- if (outPtr + len + 2 > outLength) throw new Error("Output buffer is not large enough");
146
- if (ref < 0) throw new Error("Invalid compressed data");
147
- if (ref >= outPtr) throw new Error("Invalid compressed data");
148
- do {
149
- outData[outPtr++] = outData[ref++];
150
- } while (--len + 2);
151
- }
152
- } while (inPtr < inLength);
153
- return outData;
154
- }
155
- function parseHeader(data2) {
156
- const PCDheader2 = {};
157
- const result1 = data2.search(/[\r\n]DATA\s(\S*)\s/i);
158
- const result2 = /[\r\n]DATA\s(\S*)\s/i.exec(data2.slice(result1 - 1));
159
- PCDheader2.data = result2[1];
160
- PCDheader2.headerLen = result2[0].length + result1;
161
- PCDheader2.str = data2.slice(0, PCDheader2.headerLen);
162
- PCDheader2.str = PCDheader2.str.replace(/#.*/gi, "");
163
- PCDheader2.version = /VERSION (.*)/i.exec(PCDheader2.str);
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- PCDheader2.fields = /FIELDS (.*)/i.exec(PCDheader2.str);
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- PCDheader2.size = /SIZE (.*)/i.exec(PCDheader2.str);
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- PCDheader2.type = /TYPE (.*)/i.exec(PCDheader2.str);
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- PCDheader2.count = /COUNT (.*)/i.exec(PCDheader2.str);
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- PCDheader2.width = /WIDTH (.*)/i.exec(PCDheader2.str);
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- PCDheader2.height = /HEIGHT (.*)/i.exec(PCDheader2.str);
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- PCDheader2.viewpoint = /VIEWPOINT (.*)/i.exec(PCDheader2.str);
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- PCDheader2.points = /POINTS (.*)/i.exec(PCDheader2.str);
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- if (PCDheader2.version !== null)
173
- PCDheader2.version = parseFloat(PCDheader2.version[1]);
174
- PCDheader2.fields = PCDheader2.fields !== null ? PCDheader2.fields[1].split(" ") : [];
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- if (PCDheader2.type !== null)
176
- PCDheader2.type = PCDheader2.type[1].split(" ");
177
- if (PCDheader2.width !== null)
178
- PCDheader2.width = parseInt(PCDheader2.width[1]);
179
- if (PCDheader2.height !== null)
180
- PCDheader2.height = parseInt(PCDheader2.height[1]);
181
- if (PCDheader2.viewpoint !== null)
182
- PCDheader2.viewpoint = PCDheader2.viewpoint[1];
183
- if (PCDheader2.points !== null)
184
- PCDheader2.points = parseInt(PCDheader2.points[1], 10);
185
- if (PCDheader2.points === null)
186
- PCDheader2.points = PCDheader2.width * PCDheader2.height;
187
- if (PCDheader2.size !== null) {
188
- PCDheader2.size = PCDheader2.size[1].split(" ").map(function(x) {
189
- return parseInt(x, 10);
190
- });
191
- }
192
- if (PCDheader2.count !== null) {
193
- PCDheader2.count = PCDheader2.count[1].split(" ").map(function(x) {
194
- return parseInt(x, 10);
195
- });
196
- } else {
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 + "&nbsp;&nbsp;&#9660;");
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 + "&nbsp;&nbsp;&#9660;");
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("&nbsp;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 ? "&nbsp;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>&#10697;</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-32SSD7VN.js.map