@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

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 (950) hide show
  1. package/dist/2dmaf-SLBAWGPG.js +1371 -0
  2. package/dist/AIProjectAdmin-6SH5X3AF.js +830 -0
  3. package/dist/AppHeader-MVYNRMC7.js +833 -0
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  851. /package/dist/{matrix.layout-PUNMMNCC.js.map → matrix.layout-EO5LVYRO.js.map} +0 -0
  852. /package/dist/{matrix.legend-QMERGVYU.js.map → matrix.legend-QBFBFEUG.js.map} +0 -0
  853. /package/dist/{matrix.renderers-2KQ2NXSQ.js.map → matrix.renderers-ERJXVCQL.js.map} +0 -0
  854. /package/dist/{matrix.serieses-24G3XPJD.js.map → matrix.serieses-E23EPXHA.js.map} +0 -0
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  859. /package/dist/{mavb-UGM5SHEF.js.map → mavb-5WR7OJHI.js.map} +0 -0
  860. /package/dist/{mds.fimo-64US7RTE.js.map → mds.fimo-3ZRH7BBJ.js.map} +0 -0
  861. /package/dist/{mds.samplescatterplot-JMXLXVIE.js.map → mds.samplescatterplot-RPXR2FVK.js.map} +0 -0
  862. /package/dist/{mds.survivalplot-RJ5UD3IU.js.map → mds.survivalplot-WSSMYUZD.js.map} +0 -0
  863. /package/dist/{oncomatrix.spec-4YLKDGFE.js.map → oncomatrix.spec-OEGU4DYK.js.map} +0 -0
  864. /package/dist/{plot.2dvaf-DYSU6BBN.js.map → plot.2dvaf-ZGARLQNK.js.map} +0 -0
  865. /package/dist/{plot.app-NFBVLAXZ.js.map → plot.app-TKUJH3LK.js.map} +0 -0
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  869. /package/dist/{plot.disco-VGOEQYRL.js.map → plot.disco-2KTKB3XX.js.map} +0 -0
  870. /package/dist/{plot.dzi-YQIFOTZQ.js.map → plot.dzi-PC34YI6Y.js.map} +0 -0
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  872. /package/dist/{plot.vaf2cov-KDHZ7JXJ.js.map → plot.vaf2cov-NZ4WULKT.js.map} +0 -0
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  874. /package/dist/{polar-RCCZXZIU.js.map → polar-X2GPIBLB.js.map} +0 -0
  875. /package/dist/{polar2-COQ3WIGW.js.map → polar2-TZ553QQH.js.map} +0 -0
  876. /package/dist/{profile.spec-A4ZASR2T.js.map → profile.spec-VB6VMFLY.js.map} +0 -0
  877. /package/dist/{profileBarchart-GB4RK5DF.js.map → profileBarchart-SKJSTC7B.js.map} +0 -0
  878. /package/dist/{profileForms-O5KBHRF6.js.map → profileForms-RLOGSMAQ.js.map} +0 -0
  879. /package/dist/{profilePlot-COCLCP5B.js.map → profilePlot-267ZS3RG.js.map} +0 -0
  880. /package/dist/{profileRadar-4EE3YDOH.js.map → profileRadar-KGOBHCSF.js.map} +0 -0
  881. /package/dist/{profileRadarFacility-JYTSGA5H.js.map → profileRadarFacility-MCJKSHUM.js.map} +0 -0
  882. /package/dist/{proteomeAbundance-NQVU4DOW.js.map → proteomeAbundance-JUYAYO5I.js.map} +0 -0
  883. /package/dist/{proteomeAbundance-JBVXUSD6.js.map → proteomeAbundance-PGHZSVAF.js.map} +0 -0
  884. /package/dist/{qualitative-QROOPDSI.js.map → qualitative-3IECKKJM.js.map} +0 -0
  885. /package/dist/{regression-7FQZ22OO.js.map → regression-J6FFRPXN.js.map} +0 -0
  886. /package/dist/{regression.inputs-F62CES3A.js.map → regression.inputs-T7LWBSYZ.js.map} +0 -0
  887. /package/dist/{regression.inputs.term-BCGP7PX4.js.map → regression.inputs.term-TT7PNX6G.js.map} +0 -0
  888. /package/dist/{regression.inputs.values.table-D3ZXZSH7.js.map → regression.inputs.values.table-SHFUNKCS.js.map} +0 -0
  889. /package/dist/{regression.integration.spec-P2BBTT2O.js.map → regression.integration.spec-QKHMJTHA.js.map} +0 -0
  890. /package/dist/{regression.results-JX6RJQQP.js.map → regression.results-D4WX6VIV.js.map} +0 -0
  891. /package/dist/{regression.spec-ROME7T33.js.map → regression.spec-7SW55L7X.js.map} +0 -0
  892. /package/dist/{report-B6MM4T6B.js.map → report-QYOZ4BRF.js.map} +0 -0
  893. /package/dist/{sampleScatter.spec-EPCMC3SR.js.map → sampleScatter.spec-JCHFMGNF.js.map} +0 -0
  894. /package/dist/{sampleView-77EAJ75T.js.map → sampleView-7RPKNAZC.js.map} +0 -0
  895. /package/dist/{samplelst-CX4NQWA7.js.map → samplelst-4WNPHZVG.js.map} +0 -0
  896. /package/dist/{samplematrix-PYQFAH64.js.map → samplematrix-CG52DSXJ.js.map} +0 -0
  897. /package/dist/{sc-X6SI5VVI.js.map → sc-OJSWILSA.js.map} +0 -0
  898. /package/dist/{scatter-ZFFHAI4F.js.map → scatter-LG2RMMEC.js.map} +0 -0
  899. /package/dist/{scatter.integration.spec-NN43OXRN.js.map → scatter.integration.spec-QPANYTKW.js.map} +0 -0
  900. /package/dist/{selectGenomeWithTklst-CZMVTBMD.js.map → selectGenomeWithTklst-QXRVE6N4.js.map} +0 -0
  901. /package/dist/{singleCellCellType-GOBX7JKV.js.map → singleCellCellType-XBSRL33U.js.map} +0 -0
  902. /package/dist/{singleCellCellType.unit.spec-F344QMTQ.js.map → singleCellCellType.unit.spec-YZX4CSXA.js.map} +0 -0
  903. /package/dist/{singleCellGeneExpression-BLMNMEAI.js.map → singleCellGeneExpression-64ECP62X.js.map} +0 -0
  904. /package/dist/{singleCellGeneExpression.unit.spec-6ZEPUFWC.js.map → singleCellGeneExpression.unit.spec-CFHFXMA6.js.map} +0 -0
  905. /package/dist/{singleCellPlot-HLD7PLQH.js.map → singleCellPlot-E5F62JY6.js.map} +0 -0
  906. /package/dist/{singlecell-JQFPINRS.js.map → singlecell-FCY5EOUV.js.map} +0 -0
  907. /package/dist/{singlecell-HL4GLGIA.js.map → singlecell-S7B5V7NK.js.map} +0 -0
  908. /package/dist/{snp-EAUNFDAV.js.map → snp-ACKX4GRX.js.map} +0 -0
  909. /package/dist/{snp.unit.spec-AVLPMAWI.js.map → snp.unit.spec-QBGHKKUD.js.map} +0 -0
  910. /package/dist/{snplocus-2J7OA6OL.js.map → snplocus-7EUOW7J7.js.map} +0 -0
  911. /package/dist/{spliceevent.a53ss.diagram-4DU2U7NW.js.map → spliceevent.a53ss.diagram-ALQZA35Z.js.map} +0 -0
  912. /package/dist/{spliceevent.exonskip.diagram-GG5FGXOK.js.map → spliceevent.exonskip.diagram-UF7WJA5R.js.map} +0 -0
  913. /package/dist/{spliceevent.noeventdiagram-T6RNIMCM.js.map → spliceevent.noeventdiagram-4HPGRNRR.js.map} +0 -0
  914. /package/dist/{ssGSEA-XJWLRVFQ.js.map → ssGSEA-FDRBBBLJ.js.map} +0 -0
  915. /package/dist/{ssGSEA.unit.spec-MQ23ODYO.js.map → ssGSEA.unit.spec-EZEOWJVV.js.map} +0 -0
  916. /package/dist/{summarizeCnvGeneexp-CJPC76RM.js.map → summarizeCnvGeneexp-FTL2MGAJ.js.map} +0 -0
  917. /package/dist/{summarizeGeneexpSurvival-FGCFZTVG.js.map → summarizeGeneexpSurvival-DDIF4UW6.js.map} +0 -0
  918. /package/dist/{summarizeMutationCnv-4E7R2NHQ.js.map → summarizeMutationCnv-L3GL5YDY.js.map} +0 -0
  919. /package/dist/{summarizeMutationDiagnosis-ZVX7AZK7.js.map → summarizeMutationDiagnosis-LALOJTHV.js.map} +0 -0
  920. /package/dist/{summarizeMutationSurvival-EWXD7TCT.js.map → summarizeMutationSurvival-TSNTSOBZ.js.map} +0 -0
  921. /package/dist/{summary-VUYBKQOC.js.map → summary-YRHVS64T.js.map} +0 -0
  922. /package/dist/{summary.integration.spec-EPBV5XCT.js.map → summary.integration.spec-766YQLQA.js.map} +0 -0
  923. /package/dist/{summaryInput-YX5IRGWM.js.map → summaryInput-VQ2X6GSX.js.map} +0 -0
  924. /package/dist/{sunburst-HPDML45I.js.map → sunburst-XFOONS6K.js.map} +0 -0
  925. /package/dist/{survival-E6SRRXBB.js.map → survival-FQXZH2MM.js.map} +0 -0
  926. /package/dist/{survival-XOXDPXZR.js.map → survival-TVA3ZWVP.js.map} +0 -0
  927. /package/dist/{survival.integration.spec-SJBPJZGJ.js.map → survival.integration.spec-WFIOPD6A.js.map} +0 -0
  928. /package/dist/{svgraph-D23WG3UE.js.map → svgraph-4BFBO7EL.js.map} +0 -0
  929. /package/dist/{svmr-UFC4TKWV.js.map → svmr-ML7GAIIA.js.map} +0 -0
  930. /package/dist/{table-US2K6IYZ.js.map → table-SMLMUWPP.js.map} +0 -0
  931. /package/dist/{termCollection-ZMP3VE2G.js.map → termCollection-22CPTISZ.js.map} +0 -0
  932. /package/dist/{termCollection-E7S57CIN.js.map → termCollection-EE6AOIVA.js.map} +0 -0
  933. /package/dist/{termCollection.unit.spec-MDWK6XH3.js.map → termCollection.unit.spec-4DIW3CJ3.js.map} +0 -0
  934. /package/dist/{tk-TLQJK6R4.js.map → tk-ITZCKOQ5.js.map} +0 -0
  935. /package/dist/{tp.ui-NQEAKWUH.js.map → tp.ui-R6HVKCBC.js.map} +0 -0
  936. /package/dist/{tvs.density-HSVPDDGA.js.map → tvs.density-AQ5GD437.js.map} +0 -0
  937. /package/dist/{tvs.dt-U2MINIBH.js.map → tvs.dt-2263TBEJ.js.map} +0 -0
  938. /package/dist/{tvs.dtcnv.categorical-2OOAZJKC.js.map → tvs.dtcnv.categorical-TRRHL33N.js.map} +0 -0
  939. /package/dist/{tvs.dtcnv.continuous-5ETKBJ52.js.map → tvs.dtcnv.continuous-GREYNF52.js.map} +0 -0
  940. /package/dist/{tvs.dtfusion-EB4PPR3Y.js.map → tvs.dtfusion-XOX46L3M.js.map} +0 -0
  941. /package/dist/{tvs.dtsnvindel-IRQPTKQF.js.map → tvs.dtsnvindel-IDMXT53F.js.map} +0 -0
  942. /package/dist/{tvs.dtsv-TOVXZJCR.js.map → tvs.dtsv-ZDWFYH2C.js.map} +0 -0
  943. /package/dist/{tvs.numeric-ICUGA4WY.js.map → tvs.numeric-ZN2R7BH3.js.map} +0 -0
  944. /package/dist/{tvs.samplelst-4SCH543Y.js.map → tvs.samplelst-GAP76HRH.js.map} +0 -0
  945. /package/dist/{tvs.termCollection-GGN5F6HC.js.map → tvs.termCollection-GQ65UKSI.js.map} +0 -0
  946. /package/dist/{violin-7D7DN74I.js.map → violin-JGDL62YA.js.map} +0 -0
  947. /package/dist/{violin.integration.spec-KE76AL54.js.map → violin.integration.spec-W4NN7LBY.js.map} +0 -0
  948. /package/dist/{violin.interactivity-YPJ2H6SQ.js.map → violin.interactivity-H4RP4K5U.js.map} +0 -0
  949. /package/dist/{violin.renderer-UK7WSA2Z.js.map → violin.renderer-QPHLACDC.js.map} +0 -0
  950. /package/dist/{vocabulary-KLWZ6LRP.js.map → vocabulary-7JACY4J2.js.map} +0 -0
@@ -1,1570 +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-VIYGTRUZ.js";
25
- import {
26
- schemeCategory20
27
- } from "./chunk-V2OJLJSK.js";
28
- import {
29
- findgenemodel_bysymbol,
30
- gene_searchbox
31
- } from "./chunk-JWX7GYHP.js";
32
- import "./chunk-J6XKDYNZ.js";
33
- import {
34
- appear2 as appear,
35
- disappear2 as disappear,
36
- font,
37
- newpane,
38
- sayerror
39
- } from "./chunk-XZZLEHWC.js";
40
- import "./chunk-HJ6L54YS.js";
41
- import "./chunk-CJJ6LDZM.js";
42
- import {
43
- Menu
44
- } from "./chunk-2SRMRC6L.js";
45
- import {
46
- dofetch,
47
- dofetch2
48
- } from "./chunk-QEHUEG4X.js";
49
- import "./chunk-XDI4UFCZ.js";
50
- import "./chunk-FN5XPUPH.js";
51
- import "./chunk-LSEFWW72.js";
52
- import "./chunk-5EF5U7MX.js";
53
- import "./chunk-2K5DSRBJ.js";
54
- import "./chunk-UCLS2SVB.js";
55
- import "./chunk-MVTCBVSX.js";
56
- import "./chunk-SEQLC4AD.js";
57
- import "./chunk-L4QG7XZE.js";
58
- import "./chunk-DQC5FFGV.js";
59
- import "./chunk-2TIYJ3PH.js";
60
- import "./chunk-RIGZHHCP.js";
61
- import "./chunk-AAEXTQT3.js";
62
- import "./chunk-2UWHV2SB.js";
63
- import "./chunk-ZLH4PJKX.js";
64
- import "./chunk-TV74I3Y5.js";
65
- import {
66
- area_default,
67
- line_default,
68
- monotoneX,
69
- plasma
70
- } from "./chunk-IH7ILDJS.js";
71
- import {
72
- axisBottom,
73
- axisLeft,
74
- axisTop
75
- } from "./chunk-LOZEKOES.js";
76
- import "./chunk-TOU7EVFQ.js";
77
- import {
78
- band,
79
- linear,
80
- ordinal,
81
- sequential
82
- } from "./chunk-OAWQ6LOO.js";
83
- import "./chunk-SEEYV6P2.js";
84
- import {
85
- pointer_default
86
- } from "./chunk-NDWTN4U5.js";
87
- import "./chunk-OMR2DT66.js";
88
- import "./chunk-HFNDKYVF.js";
89
-
90
- // ../node_modules/three/examples/jsm/loaders/PCDLoader.js
91
- var PCDLoader = class extends Loader {
92
- constructor(manager) {
93
- super(manager);
94
- this.littleEndian = true;
95
- }
96
- load(url, onLoad, onProgress, onError) {
97
- const scope = this;
98
- const loader = new FileLoader(scope.manager);
99
- loader.setPath(scope.path);
100
- loader.setResponseType("arraybuffer");
101
- loader.setRequestHeader(scope.requestHeader);
102
- loader.setWithCredentials(scope.withCredentials);
103
- loader.load(url, function(data) {
104
- try {
105
- onLoad(scope.parse(data));
106
- } catch (e) {
107
- if (onError) {
108
- onError(e);
109
- } else {
110
- console.error(e);
111
- }
112
- scope.manager.itemError(url);
113
- }
114
- }, onProgress, onError);
115
- }
116
- parse(data) {
117
- function decompressLZF(inData, outLength) {
118
- const inLength = inData.length;
119
- const outData = new Uint8Array(outLength);
120
- let inPtr = 0;
121
- let outPtr = 0;
122
- let ctrl;
123
- let len;
124
- let ref;
125
- do {
126
- ctrl = inData[inPtr++];
127
- if (ctrl < 1 << 5) {
128
- ctrl++;
129
- if (outPtr + ctrl > outLength) throw new Error("Output buffer is not large enough");
130
- if (inPtr + ctrl > inLength) throw new Error("Invalid compressed data");
131
- do {
132
- outData[outPtr++] = inData[inPtr++];
133
- } while (--ctrl);
134
- } else {
135
- len = ctrl >> 5;
136
- ref = outPtr - ((ctrl & 31) << 8) - 1;
137
- if (inPtr >= inLength) throw new Error("Invalid compressed data");
138
- if (len === 7) {
139
- len += inData[inPtr++];
140
- if (inPtr >= inLength) throw new Error("Invalid compressed data");
141
- }
142
- ref -= inData[inPtr++];
143
- if (outPtr + len + 2 > outLength) throw new Error("Output buffer is not large enough");
144
- if (ref < 0) throw new Error("Invalid compressed data");
145
- if (ref >= outPtr) throw new Error("Invalid compressed data");
146
- do {
147
- outData[outPtr++] = outData[ref++];
148
- } while (--len + 2);
149
- }
150
- } while (inPtr < inLength);
151
- return outData;
152
- }
153
- function parseHeader(data2) {
154
- const PCDheader2 = {};
155
- const result1 = data2.search(/[\r\n]DATA\s(\S*)\s/i);
156
- const result2 = /[\r\n]DATA\s(\S*)\s/i.exec(data2.slice(result1 - 1));
157
- PCDheader2.data = result2[1];
158
- PCDheader2.headerLen = result2[0].length + result1;
159
- PCDheader2.str = data2.slice(0, PCDheader2.headerLen);
160
- PCDheader2.str = PCDheader2.str.replace(/#.*/gi, "");
161
- PCDheader2.version = /VERSION (.*)/i.exec(PCDheader2.str);
162
- PCDheader2.fields = /FIELDS (.*)/i.exec(PCDheader2.str);
163
- PCDheader2.size = /SIZE (.*)/i.exec(PCDheader2.str);
164
- PCDheader2.type = /TYPE (.*)/i.exec(PCDheader2.str);
165
- PCDheader2.count = /COUNT (.*)/i.exec(PCDheader2.str);
166
- PCDheader2.width = /WIDTH (.*)/i.exec(PCDheader2.str);
167
- PCDheader2.height = /HEIGHT (.*)/i.exec(PCDheader2.str);
168
- PCDheader2.viewpoint = /VIEWPOINT (.*)/i.exec(PCDheader2.str);
169
- PCDheader2.points = /POINTS (.*)/i.exec(PCDheader2.str);
170
- if (PCDheader2.version !== null)
171
- PCDheader2.version = parseFloat(PCDheader2.version[1]);
172
- PCDheader2.fields = PCDheader2.fields !== null ? PCDheader2.fields[1].split(" ") : [];
173
- if (PCDheader2.type !== null)
174
- PCDheader2.type = PCDheader2.type[1].split(" ");
175
- if (PCDheader2.width !== null)
176
- PCDheader2.width = parseInt(PCDheader2.width[1]);
177
- if (PCDheader2.height !== null)
178
- PCDheader2.height = parseInt(PCDheader2.height[1]);
179
- if (PCDheader2.viewpoint !== null)
180
- PCDheader2.viewpoint = PCDheader2.viewpoint[1];
181
- if (PCDheader2.points !== null)
182
- PCDheader2.points = parseInt(PCDheader2.points[1], 10);
183
- if (PCDheader2.points === null)
184
- PCDheader2.points = PCDheader2.width * PCDheader2.height;
185
- if (PCDheader2.size !== null) {
186
- PCDheader2.size = PCDheader2.size[1].split(" ").map(function(x) {
187
- return parseInt(x, 10);
188
- });
189
- }
190
- if (PCDheader2.count !== null) {
191
- PCDheader2.count = PCDheader2.count[1].split(" ").map(function(x) {
192
- return parseInt(x, 10);
193
- });
194
- } else {
195
- PCDheader2.count = [];
196
- for (let i = 0, l = PCDheader2.fields.length; i < l; i++) {
197
- PCDheader2.count.push(1);
198
- }
199
- }
200
- PCDheader2.offset = {};
201
- let sizeSum = 0;
202
- for (let i = 0, l = PCDheader2.fields.length; i < l; i++) {
203
- if (PCDheader2.data === "ascii") {
204
- PCDheader2.offset[PCDheader2.fields[i]] = i;
205
- } else {
206
- PCDheader2.offset[PCDheader2.fields[i]] = sizeSum;
207
- sizeSum += PCDheader2.size[i] * PCDheader2.count[i];
208
- }
209
- }
210
- PCDheader2.rowSize = sizeSum;
211
- return PCDheader2;
212
- }
213
- const textData = new TextDecoder().decode(data);
214
- const PCDheader = parseHeader(textData);
215
- const position = [];
216
- const normal = [];
217
- const color = [];
218
- const intensity = [];
219
- const label = [];
220
- if (PCDheader.data === "ascii") {
221
- const offset = PCDheader.offset;
222
- const pcdData = textData.slice(PCDheader.headerLen);
223
- const lines = pcdData.split("\n");
224
- for (let i = 0, l = lines.length; i < l; i++) {
225
- if (lines[i] === "") continue;
226
- const line = lines[i].split(" ");
227
- if (offset.x !== void 0) {
228
- position.push(parseFloat(line[offset.x]));
229
- position.push(parseFloat(line[offset.y]));
230
- position.push(parseFloat(line[offset.z]));
231
- }
232
- if (offset.rgb !== void 0) {
233
- const rgb_field_index = PCDheader.fields.findIndex((field) => field === "rgb");
234
- const rgb_type = PCDheader.type[rgb_field_index];
235
- const float = parseFloat(line[offset.rgb]);
236
- let rgb = float;
237
- if (rgb_type === "F") {
238
- const farr = new Float32Array(1);
239
- farr[0] = float;
240
- rgb = new Int32Array(farr.buffer)[0];
241
- }
242
- const r = rgb >> 16 & 255;
243
- const g = rgb >> 8 & 255;
244
- const b = rgb >> 0 & 255;
245
- color.push(r / 255, g / 255, b / 255);
246
- }
247
- if (offset.normal_x !== void 0) {
248
- normal.push(parseFloat(line[offset.normal_x]));
249
- normal.push(parseFloat(line[offset.normal_y]));
250
- normal.push(parseFloat(line[offset.normal_z]));
251
- }
252
- if (offset.intensity !== void 0) {
253
- intensity.push(parseFloat(line[offset.intensity]));
254
- }
255
- if (offset.label !== void 0) {
256
- label.push(parseInt(line[offset.label]));
257
- }
258
- }
259
- }
260
- if (PCDheader.data === "binary_compressed") {
261
- const sizes = new Uint32Array(data.slice(PCDheader.headerLen, PCDheader.headerLen + 8));
262
- const compressedSize = sizes[0];
263
- const decompressedSize = sizes[1];
264
- const decompressed = decompressLZF(new Uint8Array(data, PCDheader.headerLen + 8, compressedSize), decompressedSize);
265
- const dataview = new DataView(decompressed.buffer);
266
- const offset = PCDheader.offset;
267
- for (let i = 0; i < PCDheader.points; i++) {
268
- if (offset.x !== void 0) {
269
- const xIndex = PCDheader.fields.indexOf("x");
270
- const yIndex = PCDheader.fields.indexOf("y");
271
- const zIndex = PCDheader.fields.indexOf("z");
272
- position.push(dataview.getFloat32(PCDheader.points * offset.x + PCDheader.size[xIndex] * i, this.littleEndian));
273
- position.push(dataview.getFloat32(PCDheader.points * offset.y + PCDheader.size[yIndex] * i, this.littleEndian));
274
- position.push(dataview.getFloat32(PCDheader.points * offset.z + PCDheader.size[zIndex] * i, this.littleEndian));
275
- }
276
- if (offset.rgb !== void 0) {
277
- const rgbIndex = PCDheader.fields.indexOf("rgb");
278
- color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[rgbIndex] * i + 2) / 255);
279
- color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[rgbIndex] * i + 1) / 255);
280
- color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[rgbIndex] * i + 0) / 255);
281
- }
282
- if (offset.normal_x !== void 0) {
283
- const xIndex = PCDheader.fields.indexOf("normal_x");
284
- const yIndex = PCDheader.fields.indexOf("normal_y");
285
- const zIndex = PCDheader.fields.indexOf("normal_z");
286
- normal.push(dataview.getFloat32(PCDheader.points * offset.normal_x + PCDheader.size[xIndex] * i, this.littleEndian));
287
- normal.push(dataview.getFloat32(PCDheader.points * offset.normal_y + PCDheader.size[yIndex] * i, this.littleEndian));
288
- normal.push(dataview.getFloat32(PCDheader.points * offset.normal_z + PCDheader.size[zIndex] * i, this.littleEndian));
289
- }
290
- if (offset.intensity !== void 0) {
291
- const intensityIndex = PCDheader.fields.indexOf("intensity");
292
- intensity.push(dataview.getFloat32(PCDheader.points * offset.intensity + PCDheader.size[intensityIndex] * i, this.littleEndian));
293
- }
294
- if (offset.label !== void 0) {
295
- const labelIndex = PCDheader.fields.indexOf("label");
296
- label.push(dataview.getInt32(PCDheader.points * offset.label + PCDheader.size[labelIndex] * i, this.littleEndian));
297
- }
298
- }
299
- }
300
- if (PCDheader.data === "binary") {
301
- const dataview = new DataView(data, PCDheader.headerLen);
302
- const offset = PCDheader.offset;
303
- for (let i = 0, row = 0; i < PCDheader.points; i++, row += PCDheader.rowSize) {
304
- if (offset.x !== void 0) {
305
- position.push(dataview.getFloat32(row + offset.x, this.littleEndian));
306
- position.push(dataview.getFloat32(row + offset.y, this.littleEndian));
307
- position.push(dataview.getFloat32(row + offset.z, this.littleEndian));
308
- }
309
- if (offset.rgb !== void 0) {
310
- color.push(dataview.getUint8(row + offset.rgb + 2) / 255);
311
- color.push(dataview.getUint8(row + offset.rgb + 1) / 255);
312
- color.push(dataview.getUint8(row + offset.rgb + 0) / 255);
313
- }
314
- if (offset.normal_x !== void 0) {
315
- normal.push(dataview.getFloat32(row + offset.normal_x, this.littleEndian));
316
- normal.push(dataview.getFloat32(row + offset.normal_y, this.littleEndian));
317
- normal.push(dataview.getFloat32(row + offset.normal_z, this.littleEndian));
318
- }
319
- if (offset.intensity !== void 0) {
320
- intensity.push(dataview.getFloat32(row + offset.intensity, this.littleEndian));
321
- }
322
- if (offset.label !== void 0) {
323
- label.push(dataview.getInt32(row + offset.label, this.littleEndian));
324
- }
325
- }
326
- }
327
- const geometry = new BufferGeometry();
328
- if (position.length > 0) geometry.setAttribute("position", new Float32BufferAttribute(position, 3));
329
- if (normal.length > 0) geometry.setAttribute("normal", new Float32BufferAttribute(normal, 3));
330
- if (color.length > 0) geometry.setAttribute("color", new Float32BufferAttribute(color, 3));
331
- if (intensity.length > 0) geometry.setAttribute("intensity", new Float32BufferAttribute(intensity, 1));
332
- if (label.length > 0) geometry.setAttribute("label", new Int32BufferAttribute(label, 1));
333
- geometry.computeBoundingSphere();
334
- const material = new PointsMaterial({ size: 5e-3 });
335
- if (color.length > 0) {
336
- material.vertexColors = true;
337
- }
338
- return new Points(geometry, material);
339
- }
340
- };
341
-
342
- // ../public/static/js/WebGL.js
343
- function isWebGLAvailable() {
344
- try {
345
- var canvas = document.createElement("canvas");
346
- return !!(window.WebGLRenderingContext && (canvas.getContext("webgl") || canvas.getContext("experimental-webgl")));
347
- } catch (e) {
348
- return false;
349
- }
350
- }
351
- function getWebGLErrorMessage() {
352
- return this.getErrorMessage(1);
353
- }
354
-
355
- // ../node_modules/three/examples/jsm/controls/TrackballControls.js
356
- var _changeEvent = { type: "change" };
357
- var _startEvent = { type: "start" };
358
- var _endEvent = { type: "end" };
359
- var TrackballControls = class extends EventDispatcher {
360
- constructor(object, domElement) {
361
- super();
362
- const scope = this;
363
- const STATE = { NONE: -1, ROTATE: 0, ZOOM: 1, PAN: 2, TOUCH_ROTATE: 3, TOUCH_ZOOM_PAN: 4 };
364
- this.object = object;
365
- this.domElement = domElement;
366
- this.domElement.style.touchAction = "none";
367
- this.enabled = true;
368
- this.screen = { left: 0, top: 0, width: 0, height: 0 };
369
- this.rotateSpeed = 1;
370
- this.zoomSpeed = 1.2;
371
- this.panSpeed = 0.3;
372
- this.noRotate = false;
373
- this.noZoom = false;
374
- this.noPan = false;
375
- this.staticMoving = false;
376
- this.dynamicDampingFactor = 0.2;
377
- this.minDistance = 0;
378
- this.maxDistance = Infinity;
379
- this.minZoom = 0;
380
- this.maxZoom = Infinity;
381
- this.keys = [
382
- "KeyA",
383
- "KeyS",
384
- "KeyD"
385
- /*D*/
386
- ];
387
- this.mouseButtons = { LEFT: MOUSE.ROTATE, MIDDLE: MOUSE.DOLLY, RIGHT: MOUSE.PAN };
388
- this.target = new Vector3();
389
- const EPS = 1e-6;
390
- const lastPosition = new Vector3();
391
- let lastZoom = 1;
392
- let _state = STATE.NONE, _keyState = STATE.NONE, _touchZoomDistanceStart = 0, _touchZoomDistanceEnd = 0, _lastAngle = 0;
393
- 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 = {};
394
- this.target0 = this.target.clone();
395
- this.position0 = this.object.position.clone();
396
- this.up0 = this.object.up.clone();
397
- this.zoom0 = this.object.zoom;
398
- this.handleResize = function() {
399
- const box = scope.domElement.getBoundingClientRect();
400
- const d = scope.domElement.ownerDocument.documentElement;
401
- scope.screen.left = box.left + window.pageXOffset - d.clientLeft;
402
- scope.screen.top = box.top + window.pageYOffset - d.clientTop;
403
- scope.screen.width = box.width;
404
- scope.screen.height = box.height;
405
- };
406
- const getMouseOnScreen = (function() {
407
- const vector = new Vector2();
408
- return function getMouseOnScreen2(pageX, pageY) {
409
- vector.set(
410
- (pageX - scope.screen.left) / scope.screen.width,
411
- (pageY - scope.screen.top) / scope.screen.height
412
- );
413
- return vector;
414
- };
415
- })();
416
- const getMouseOnCircle = (function() {
417
- const vector = new Vector2();
418
- return function getMouseOnCircle2(pageX, pageY) {
419
- vector.set(
420
- (pageX - scope.screen.width * 0.5 - scope.screen.left) / (scope.screen.width * 0.5),
421
- (scope.screen.height + 2 * (scope.screen.top - pageY)) / scope.screen.width
422
- // screen.width intentional
423
- );
424
- return vector;
425
- };
426
- })();
427
- this.rotateCamera = (function() {
428
- const axis = new Vector3(), quaternion = new Quaternion(), eyeDirection = new Vector3(), objectUpDirection = new Vector3(), objectSidewaysDirection = new Vector3(), moveDirection = new Vector3();
429
- return function rotateCamera() {
430
- moveDirection.set(_moveCurr.x - _movePrev.x, _moveCurr.y - _movePrev.y, 0);
431
- let angle = moveDirection.length();
432
- if (angle) {
433
- _eye.copy(scope.object.position).sub(scope.target);
434
- eyeDirection.copy(_eye).normalize();
435
- objectUpDirection.copy(scope.object.up).normalize();
436
- objectSidewaysDirection.crossVectors(objectUpDirection, eyeDirection).normalize();
437
- objectUpDirection.setLength(_moveCurr.y - _movePrev.y);
438
- objectSidewaysDirection.setLength(_moveCurr.x - _movePrev.x);
439
- moveDirection.copy(objectUpDirection.add(objectSidewaysDirection));
440
- axis.crossVectors(moveDirection, _eye).normalize();
441
- angle *= scope.rotateSpeed;
442
- quaternion.setFromAxisAngle(axis, angle);
443
- _eye.applyQuaternion(quaternion);
444
- scope.object.up.applyQuaternion(quaternion);
445
- _lastAxis.copy(axis);
446
- _lastAngle = angle;
447
- } else if (!scope.staticMoving && _lastAngle) {
448
- _lastAngle *= Math.sqrt(1 - scope.dynamicDampingFactor);
449
- _eye.copy(scope.object.position).sub(scope.target);
450
- quaternion.setFromAxisAngle(_lastAxis, _lastAngle);
451
- _eye.applyQuaternion(quaternion);
452
- scope.object.up.applyQuaternion(quaternion);
453
- }
454
- _movePrev.copy(_moveCurr);
455
- };
456
- })();
457
- this.zoomCamera = function() {
458
- let factor;
459
- if (_state === STATE.TOUCH_ZOOM_PAN) {
460
- factor = _touchZoomDistanceStart / _touchZoomDistanceEnd;
461
- _touchZoomDistanceStart = _touchZoomDistanceEnd;
462
- if (scope.object.isPerspectiveCamera) {
463
- _eye.multiplyScalar(factor);
464
- } else if (scope.object.isOrthographicCamera) {
465
- scope.object.zoom = MathUtils.clamp(scope.object.zoom / factor, scope.minZoom, scope.maxZoom);
466
- if (lastZoom !== scope.object.zoom) {
467
- scope.object.updateProjectionMatrix();
468
- }
469
- } else {
470
- console.warn("THREE.TrackballControls: Unsupported camera type");
471
- }
472
- } else {
473
- factor = 1 + (_zoomEnd.y - _zoomStart.y) * scope.zoomSpeed;
474
- if (factor !== 1 && factor > 0) {
475
- if (scope.object.isPerspectiveCamera) {
476
- _eye.multiplyScalar(factor);
477
- } else if (scope.object.isOrthographicCamera) {
478
- scope.object.zoom = MathUtils.clamp(scope.object.zoom / factor, scope.minZoom, scope.maxZoom);
479
- if (lastZoom !== scope.object.zoom) {
480
- scope.object.updateProjectionMatrix();
481
- }
482
- } else {
483
- console.warn("THREE.TrackballControls: Unsupported camera type");
484
- }
485
- }
486
- if (scope.staticMoving) {
487
- _zoomStart.copy(_zoomEnd);
488
- } else {
489
- _zoomStart.y += (_zoomEnd.y - _zoomStart.y) * this.dynamicDampingFactor;
490
- }
491
- }
492
- };
493
- this.panCamera = (function() {
494
- const mouseChange = new Vector2(), objectUp = new Vector3(), pan = new Vector3();
495
- return function panCamera() {
496
- mouseChange.copy(_panEnd).sub(_panStart);
497
- if (mouseChange.lengthSq()) {
498
- if (scope.object.isOrthographicCamera) {
499
- const scale_x = (scope.object.right - scope.object.left) / scope.object.zoom / scope.domElement.clientWidth;
500
- const scale_y = (scope.object.top - scope.object.bottom) / scope.object.zoom / scope.domElement.clientWidth;
501
- mouseChange.x *= scale_x;
502
- mouseChange.y *= scale_y;
503
- }
504
- mouseChange.multiplyScalar(_eye.length() * scope.panSpeed);
505
- pan.copy(_eye).cross(scope.object.up).setLength(mouseChange.x);
506
- pan.add(objectUp.copy(scope.object.up).setLength(mouseChange.y));
507
- scope.object.position.add(pan);
508
- scope.target.add(pan);
509
- if (scope.staticMoving) {
510
- _panStart.copy(_panEnd);
511
- } else {
512
- _panStart.add(mouseChange.subVectors(_panEnd, _panStart).multiplyScalar(scope.dynamicDampingFactor));
513
- }
514
- }
515
- };
516
- })();
517
- this.checkDistances = function() {
518
- if (!scope.noZoom || !scope.noPan) {
519
- if (_eye.lengthSq() > scope.maxDistance * scope.maxDistance) {
520
- scope.object.position.addVectors(scope.target, _eye.setLength(scope.maxDistance));
521
- _zoomStart.copy(_zoomEnd);
522
- }
523
- if (_eye.lengthSq() < scope.minDistance * scope.minDistance) {
524
- scope.object.position.addVectors(scope.target, _eye.setLength(scope.minDistance));
525
- _zoomStart.copy(_zoomEnd);
526
- }
527
- }
528
- };
529
- this.update = function() {
530
- _eye.subVectors(scope.object.position, scope.target);
531
- if (!scope.noRotate) {
532
- scope.rotateCamera();
533
- }
534
- if (!scope.noZoom) {
535
- scope.zoomCamera();
536
- }
537
- if (!scope.noPan) {
538
- scope.panCamera();
539
- }
540
- scope.object.position.addVectors(scope.target, _eye);
541
- if (scope.object.isPerspectiveCamera) {
542
- scope.checkDistances();
543
- scope.object.lookAt(scope.target);
544
- if (lastPosition.distanceToSquared(scope.object.position) > EPS) {
545
- scope.dispatchEvent(_changeEvent);
546
- lastPosition.copy(scope.object.position);
547
- }
548
- } else if (scope.object.isOrthographicCamera) {
549
- scope.object.lookAt(scope.target);
550
- if (lastPosition.distanceToSquared(scope.object.position) > EPS || lastZoom !== scope.object.zoom) {
551
- scope.dispatchEvent(_changeEvent);
552
- lastPosition.copy(scope.object.position);
553
- lastZoom = scope.object.zoom;
554
- }
555
- } else {
556
- console.warn("THREE.TrackballControls: Unsupported camera type");
557
- }
558
- };
559
- this.reset = function() {
560
- _state = STATE.NONE;
561
- _keyState = STATE.NONE;
562
- scope.target.copy(scope.target0);
563
- scope.object.position.copy(scope.position0);
564
- scope.object.up.copy(scope.up0);
565
- scope.object.zoom = scope.zoom0;
566
- scope.object.updateProjectionMatrix();
567
- _eye.subVectors(scope.object.position, scope.target);
568
- scope.object.lookAt(scope.target);
569
- scope.dispatchEvent(_changeEvent);
570
- lastPosition.copy(scope.object.position);
571
- lastZoom = scope.object.zoom;
572
- };
573
- function onPointerDown(event) {
574
- if (scope.enabled === false) return;
575
- if (_pointers.length === 0) {
576
- scope.domElement.setPointerCapture(event.pointerId);
577
- scope.domElement.addEventListener("pointermove", onPointerMove);
578
- scope.domElement.addEventListener("pointerup", onPointerUp);
579
- }
580
- addPointer(event);
581
- if (event.pointerType === "touch") {
582
- onTouchStart(event);
583
- } else {
584
- onMouseDown(event);
585
- }
586
- }
587
- function onPointerMove(event) {
588
- if (scope.enabled === false) return;
589
- if (event.pointerType === "touch") {
590
- onTouchMove(event);
591
- } else {
592
- onMouseMove(event);
593
- }
594
- }
595
- function onPointerUp(event) {
596
- if (scope.enabled === false) return;
597
- if (event.pointerType === "touch") {
598
- onTouchEnd(event);
599
- } else {
600
- onMouseUp();
601
- }
602
- removePointer(event);
603
- if (_pointers.length === 0) {
604
- scope.domElement.releasePointerCapture(event.pointerId);
605
- scope.domElement.removeEventListener("pointermove", onPointerMove);
606
- scope.domElement.removeEventListener("pointerup", onPointerUp);
607
- }
608
- }
609
- function onPointerCancel(event) {
610
- removePointer(event);
611
- }
612
- function keydown(event) {
613
- if (scope.enabled === false) return;
614
- window.removeEventListener("keydown", keydown);
615
- if (_keyState !== STATE.NONE) {
616
- return;
617
- } else if (event.code === scope.keys[STATE.ROTATE] && !scope.noRotate) {
618
- _keyState = STATE.ROTATE;
619
- } else if (event.code === scope.keys[STATE.ZOOM] && !scope.noZoom) {
620
- _keyState = STATE.ZOOM;
621
- } else if (event.code === scope.keys[STATE.PAN] && !scope.noPan) {
622
- _keyState = STATE.PAN;
623
- }
624
- }
625
- function keyup() {
626
- if (scope.enabled === false) return;
627
- _keyState = STATE.NONE;
628
- window.addEventListener("keydown", keydown);
629
- }
630
- function onMouseDown(event) {
631
- if (_state === STATE.NONE) {
632
- switch (event.button) {
633
- case scope.mouseButtons.LEFT:
634
- _state = STATE.ROTATE;
635
- break;
636
- case scope.mouseButtons.MIDDLE:
637
- _state = STATE.ZOOM;
638
- break;
639
- case scope.mouseButtons.RIGHT:
640
- _state = STATE.PAN;
641
- break;
642
- }
643
- }
644
- const state = _keyState !== STATE.NONE ? _keyState : _state;
645
- if (state === STATE.ROTATE && !scope.noRotate) {
646
- _moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
647
- _movePrev.copy(_moveCurr);
648
- } else if (state === STATE.ZOOM && !scope.noZoom) {
649
- _zoomStart.copy(getMouseOnScreen(event.pageX, event.pageY));
650
- _zoomEnd.copy(_zoomStart);
651
- } else if (state === STATE.PAN && !scope.noPan) {
652
- _panStart.copy(getMouseOnScreen(event.pageX, event.pageY));
653
- _panEnd.copy(_panStart);
654
- }
655
- scope.dispatchEvent(_startEvent);
656
- }
657
- function onMouseMove(event) {
658
- const state = _keyState !== STATE.NONE ? _keyState : _state;
659
- if (state === STATE.ROTATE && !scope.noRotate) {
660
- _movePrev.copy(_moveCurr);
661
- _moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
662
- } else if (state === STATE.ZOOM && !scope.noZoom) {
663
- _zoomEnd.copy(getMouseOnScreen(event.pageX, event.pageY));
664
- } else if (state === STATE.PAN && !scope.noPan) {
665
- _panEnd.copy(getMouseOnScreen(event.pageX, event.pageY));
666
- }
667
- }
668
- function onMouseUp() {
669
- _state = STATE.NONE;
670
- scope.dispatchEvent(_endEvent);
671
- }
672
- function onMouseWheel(event) {
673
- if (scope.enabled === false) return;
674
- if (scope.noZoom === true) return;
675
- event.preventDefault();
676
- switch (event.deltaMode) {
677
- case 2:
678
- _zoomStart.y -= event.deltaY * 0.025;
679
- break;
680
- case 1:
681
- _zoomStart.y -= event.deltaY * 0.01;
682
- break;
683
- default:
684
- _zoomStart.y -= event.deltaY * 25e-5;
685
- break;
686
- }
687
- scope.dispatchEvent(_startEvent);
688
- scope.dispatchEvent(_endEvent);
689
- }
690
- function onTouchStart(event) {
691
- trackPointer(event);
692
- switch (_pointers.length) {
693
- case 1:
694
- _state = STATE.TOUCH_ROTATE;
695
- _moveCurr.copy(getMouseOnCircle(_pointers[0].pageX, _pointers[0].pageY));
696
- _movePrev.copy(_moveCurr);
697
- break;
698
- default:
699
- _state = STATE.TOUCH_ZOOM_PAN;
700
- const dx = _pointers[0].pageX - _pointers[1].pageX;
701
- const dy = _pointers[0].pageY - _pointers[1].pageY;
702
- _touchZoomDistanceEnd = _touchZoomDistanceStart = Math.sqrt(dx * dx + dy * dy);
703
- const x = (_pointers[0].pageX + _pointers[1].pageX) / 2;
704
- const y = (_pointers[0].pageY + _pointers[1].pageY) / 2;
705
- _panStart.copy(getMouseOnScreen(x, y));
706
- _panEnd.copy(_panStart);
707
- break;
708
- }
709
- scope.dispatchEvent(_startEvent);
710
- }
711
- function onTouchMove(event) {
712
- trackPointer(event);
713
- switch (_pointers.length) {
714
- case 1:
715
- _movePrev.copy(_moveCurr);
716
- _moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
717
- break;
718
- default:
719
- const position = getSecondPointerPosition(event);
720
- const dx = event.pageX - position.x;
721
- const dy = event.pageY - position.y;
722
- _touchZoomDistanceEnd = Math.sqrt(dx * dx + dy * dy);
723
- const x = (event.pageX + position.x) / 2;
724
- const y = (event.pageY + position.y) / 2;
725
- _panEnd.copy(getMouseOnScreen(x, y));
726
- break;
727
- }
728
- }
729
- function onTouchEnd(event) {
730
- switch (_pointers.length) {
731
- case 0:
732
- _state = STATE.NONE;
733
- break;
734
- case 1:
735
- _state = STATE.TOUCH_ROTATE;
736
- _moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
737
- _movePrev.copy(_moveCurr);
738
- break;
739
- case 2:
740
- _state = STATE.TOUCH_ZOOM_PAN;
741
- for (let i = 0; i < _pointers.length; i++) {
742
- if (_pointers[i].pointerId !== event.pointerId) {
743
- const position = _pointerPositions[_pointers[i].pointerId];
744
- _moveCurr.copy(getMouseOnCircle(position.x, position.y));
745
- _movePrev.copy(_moveCurr);
746
- break;
747
- }
748
- }
749
- break;
750
- }
751
- scope.dispatchEvent(_endEvent);
752
- }
753
- function contextmenu(event) {
754
- if (scope.enabled === false) return;
755
- event.preventDefault();
756
- }
757
- function addPointer(event) {
758
- _pointers.push(event);
759
- }
760
- function removePointer(event) {
761
- delete _pointerPositions[event.pointerId];
762
- for (let i = 0; i < _pointers.length; i++) {
763
- if (_pointers[i].pointerId == event.pointerId) {
764
- _pointers.splice(i, 1);
765
- return;
766
- }
767
- }
768
- }
769
- function trackPointer(event) {
770
- let position = _pointerPositions[event.pointerId];
771
- if (position === void 0) {
772
- position = new Vector2();
773
- _pointerPositions[event.pointerId] = position;
774
- }
775
- position.set(event.pageX, event.pageY);
776
- }
777
- function getSecondPointerPosition(event) {
778
- const pointer = event.pointerId === _pointers[0].pointerId ? _pointers[1] : _pointers[0];
779
- return _pointerPositions[pointer.pointerId];
780
- }
781
- this.dispose = function() {
782
- scope.domElement.removeEventListener("contextmenu", contextmenu);
783
- scope.domElement.removeEventListener("pointerdown", onPointerDown);
784
- scope.domElement.removeEventListener("pointercancel", onPointerCancel);
785
- scope.domElement.removeEventListener("wheel", onMouseWheel);
786
- scope.domElement.removeEventListener("pointermove", onPointerMove);
787
- scope.domElement.removeEventListener("pointerup", onPointerUp);
788
- window.removeEventListener("keydown", keydown);
789
- window.removeEventListener("keyup", keyup);
790
- };
791
- this.domElement.addEventListener("contextmenu", contextmenu);
792
- this.domElement.addEventListener("pointerdown", onPointerDown);
793
- this.domElement.addEventListener("pointercancel", onPointerCancel);
794
- this.domElement.addEventListener("wheel", onMouseWheel, { passive: false });
795
- window.addEventListener("keydown", keydown);
796
- window.addEventListener("keyup", keyup);
797
- this.handleResize();
798
- this.update();
799
- }
800
- };
801
-
802
- // src/singlecell.js
803
- async function init(arg, holder) {
804
- try {
805
- const obj = await load_json(arg);
806
- validate_obj(obj);
807
- obj.genome = arg.genome;
808
- obj.holder = holder.style("position", "relative");
809
- await init_view(obj);
810
- init_controlpanel(obj);
811
- await pcd_pipeline(obj);
812
- make_legend(arg, obj);
813
- } catch (e) {
814
- sayerror(holder, e.message || e);
815
- }
816
- }
817
- async function load_json(arg) {
818
- if (!arg.jsonfile) throw ".jsonfile missing";
819
- const tmp = await dofetch("textfile", { file: arg.jsonfile });
820
- if (tmp.error) throw tmp.error;
821
- return JSON.parse(tmp.text);
822
- }
823
- function validate_obj(obj) {
824
- if (!obj.cells) throw ".cells{} missing";
825
- if (!obj.cells.file) throw ".cells.file missing";
826
- if (!obj.cells.axis2columnidx) throw ".cells.axis2columnidx missing";
827
- if (obj.cells.categories) {
828
- if (!Array.isArray(obj.cells.categories)) throw ".cells.categories should be an array";
829
- if (obj.cells.categories.length == 0) throw ".cells.categories[] is empty array";
830
- for (const c of obj.cells.categories) {
831
- if (!Number.isInteger(c.columnidx)) throw "columnidx missing from category " + c;
832
- if (c.autocolor) {
833
- c.autocolor = ordinal(schemeCategory20);
834
- }
835
- }
836
- if (!Number.isInteger(obj.use_category_index)) {
837
- obj.use_category_index = 0;
838
- }
839
- if (!obj.cells.categories[obj.use_category_index]) throw "use_category_index out of bound";
840
- if (!obj.cells.categories[obj.use_category_index].hidden_types)
841
- obj.cells.categories[obj.use_category_index].hidden_types = [];
842
- }
843
- if (obj.gene_expression) {
844
- if (!obj.gene_expression.file) throw ".gene_expression.file missing";
845
- if (!Number.isInteger(obj.cells.barcodecolumnidx))
846
- throw ".gene_expression in use but .cells.barcodecolumnidx is missing";
847
- }
848
- if (!obj.width) obj.width = window.innerWidth * 0.9;
849
- if (!obj.height) obj.height = window.innerHeight * 0.9;
850
- }
851
- async function pcd_pipeline(obj) {
852
- if (Number.isInteger(obj.use_category_index)) {
853
- if (!obj.cells.categories[obj.use_category_index].hidden_types)
854
- obj.cells.categories[obj.use_category_index].hidden_types = [];
855
- }
856
- const data = await load_cell_pcd(obj);
857
- obj.data_sphere_r = data.data_sphere_r;
858
- if (!obj.camera.position.z) {
859
- obj.camera.position.z = obj.data_sphere_r * 3;
860
- obj.controls.maxDistance = obj.data_sphere_r * 4;
861
- obj.controls.minDistance = obj.data_sphere_r / 10;
862
- }
863
- const enc = new TextEncoder();
864
- const pcd_buffer = enc.encode(data.pcddata).buffer;
865
- render_cloud(obj, pcd_buffer);
866
- render_controlpanel(obj, data);
867
- animate();
868
- function animate() {
869
- requestAnimationFrame(animate);
870
- obj.controls.update();
871
- obj.renderer.render(obj.scene, obj.camera);
872
- }
873
- }
874
- async function load_cell_pcd(obj) {
875
- 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...");
876
- const arg = {
877
- genome: obj.genome.name,
878
- textfile: obj.cells.file,
879
- delimiter: obj.cells.delimiter || " ",
880
- getpcd: {
881
- coord: obj.cells.axis2columnidx
882
- }
883
- };
884
- if (Number.isInteger(obj.use_category_index)) {
885
- if (!obj.cells.categories) throw "using category index but cells.categories[] missing";
886
- const cat = obj.cells.categories[obj.use_category_index];
887
- if (!cat) throw "category array index out of bound";
888
- arg.getpcd.category_index = cat.columnidx;
889
- if (cat.autocolor) {
890
- arg.getpcd.category_autocolor = true;
891
- if (cat.values_count) arg.getpcd.values_count = cat.values_count;
892
- } else if (cat.values) {
893
- arg.getpcd.category_customcolor = true;
894
- arg.getpcd.cat_values = cat.values;
895
- } else {
896
- if (!cat.autocolor && !cat.values) throw "categories.values[] are not defined";
897
- throw "unknow coloring scheme for category " + cat.name;
898
- }
899
- if (cat.hidden_types) {
900
- arg.hidden_types = cat.hidden_types;
901
- }
902
- if (obj.background_color) {
903
- arg.background_color = obj.background_color;
904
- }
905
- if (!cat.customorder) {
906
- arg.getpcd.category_autoorder = true;
907
- } else if (cat.customorder && cat.values) {
908
- arg.getpcd.category_customorder = true;
909
- arg.getpcd.cat_values = cat.values;
910
- } else {
911
- if (cat.customorder && !cat.values) throw "categories.values[] are not defined";
912
- throw "unknow ordering scheme for category " + cat.name;
913
- }
914
- obj.menu_button.html(cat.name + "&nbsp;&nbsp;&#9660;");
915
- } else if (Number.isInteger(obj.use_gene_index)) {
916
- const gene = obj.gene_expression.genes[obj.use_gene_index];
917
- obj.menu_button.html("Gene : " + gene.gene + "&nbsp;&nbsp;&#9660;");
918
- arg.getpcd.gene_expression = {
919
- file: obj.gene_expression.file,
920
- barcodecolumnidx: obj.cells.barcodecolumnidx,
921
- chr: gene.chr,
922
- start: gene.start,
923
- stop: gene.stop,
924
- autoscale: true,
925
- genename: gene.gene,
926
- color_min: obj.gene_expression.color_min,
927
- color_max: obj.gene_expression.color_max
928
- };
929
- if (obj.gene_expression.color_no_exp) arg.getpcd.gene_expression.color_no_exp = obj.gene_expression.color_no_exp;
930
- } else {
931
- throw "unknown method to color the cells";
932
- }
933
- return dofetch("singlecell", arg).then((data) => {
934
- if (data.error) throw data.error;
935
- wait.remove();
936
- return data;
937
- });
938
- }
939
- async function init_view(obj) {
940
- if (isWebGLAvailable() === false) {
941
- obj.holder.node().appendChild(getWebGLErrorMessage());
942
- return;
943
- }
944
- obj.scene = new Scene();
945
- if (obj.background_color) {
946
- obj.scene.background = new Color(obj.background_color);
947
- } else {
948
- obj.scene.background = new Color(16777215);
949
- }
950
- const default_zoom = obj.default_zoom ? 100 - obj.default_zoom : 45;
951
- obj.camera = new PerspectiveCamera(default_zoom, obj.width / obj.height, 0.1, 1e3);
952
- obj.camera.position.x = obj.canvas_2d ? 0 : 20;
953
- obj.camera.position.y = obj.canvas_2d ? 0 : -10;
954
- if (obj.canvas_2d) {
955
- obj.camera.up.set(0, 1, 0);
956
- } else {
957
- obj.camera.up.set(0, 0, 1);
958
- }
959
- obj.renderer = new WebGLRenderer({ antialias: true, preserveDrawingBuffer: true });
960
- obj.renderer.setPixelRatio(window.devicePixelRatio);
961
- obj.renderer.setSize(obj.width, obj.height);
962
- obj.renderer.domElement.style.backgroundColor = "#ffffff";
963
- obj.renderer.domElement.style.border = "solid #dddddd 2px";
964
- obj.renderer.outputColorSpace = LinearSRGBColorSpace;
965
- obj.renderer.toneMapping = NoToneMapping;
966
- obj.holder.style("display", "inline-block").style("position", "relative").node().appendChild(obj.renderer.domElement);
967
- obj.controls = new TrackballControls(obj.camera, obj.renderer.domElement);
968
- obj.controls.rotateSpeed = obj.canvas_2d ? 0 : 2;
969
- obj.controls.zoomSpeed = obj.canvas_2d ? 3 : 0.7;
970
- obj.controls.panSpeed = obj.canvas_2d ? 3 : 0.7;
971
- obj.controls.noZoom = true;
972
- obj.controls.noPan = false;
973
- obj.controls.staticMoving = true;
974
- obj.controls.dynamicDampingFactor = 0.3;
975
- obj.scene.add(obj.camera);
976
- obj.renderer.render(obj.scene, obj.camera);
977
- obj.controls.update();
978
- }
979
- function render_cloud(obj, pcd_buffer) {
980
- obj.scene.children.forEach(function(v, i) {
981
- if (v.material) {
982
- v.material.dispose();
983
- v.geometry.dispose();
984
- obj.scene.remove(v);
985
- }
986
- });
987
- const loader = new PCDLoader();
988
- const points = loader.parse(pcd_buffer, "");
989
- const newMat = new PointsMaterial({
990
- size: points.material.size,
991
- vertexColors: true,
992
- color: 16777215
993
- });
994
- points.material = newMat;
995
- points.material.vertexColors = true;
996
- points.material.color.set(16777215);
997
- points.material.needsUpdate = true;
998
- if (obj.point_size) {
999
- points.material.size = obj.point_size;
1000
- } else {
1001
- points.material.size = obj.canvas_2d ? 0.3 : 0.05;
1002
- }
1003
- obj.scene.add(points);
1004
- obj.center = points.geometry.boundingSphere.center;
1005
- obj.controls.target.set(obj.center.x, obj.center.y, obj.center.z);
1006
- obj.controls.update();
1007
- }
1008
- function init_controlpanel(obj) {
1009
- obj.menu = new Menu();
1010
- obj.menu.d.style("padding", "3px");
1011
- obj.settings = new Menu();
1012
- obj.settings.d.style("padding", "3px");
1013
- 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");
1014
- obj.menu_button = panel.append("button").style("display", "inline-block").style("padding", "4px").on("click", () => make_menu(obj));
1015
- 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", () => {
1016
- obj.minimize_btn.classed("active", obj.minimize_btn.classed("active") ? false : true);
1017
- if (obj.minimize_btn.classed("active")) {
1018
- obj.minimize_btn.text(" SHOW");
1019
- obj.menu_output.style("display", "none");
1020
- } else {
1021
- obj.minimize_btn.text(" HIDE");
1022
- obj.menu_output.style("display", "block");
1023
- }
1024
- }).on("mouseover", () => {
1025
- minimize_btn.style("text-decoration", "underline");
1026
- }).on("mouseout", () => {
1027
- minimize_btn.style("text-decoration", "none");
1028
- });
1029
- obj.use_background_color = 0;
1030
- 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", () => {
1031
- config_btn.style("text-decoration", "underline");
1032
- }).on("mouseout", () => {
1033
- config_btn.style("text-decoration", "none");
1034
- });
1035
- obj.menu_output = panel.append("div").style("margin-top", "10px").style("display", obj.menu_minimized ? "none" : "block");
1036
- obj.show_zoom = true;
1037
- }
1038
- function render_controlpanel(obj, data) {
1039
- obj.menu_output.selectAll("*").remove();
1040
- if (data.category2color) {
1041
- const top_row = obj.menu_output.append("div").style("margin", "2px");
1042
- 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", () => {
1043
- if (select_all_checkbox.node().checked) {
1044
- obj.cells.categories[obj.use_category_index].hidden_types = [];
1045
- pcd_pipeline(obj);
1046
- } else {
1047
- for (const type in data.category2color) {
1048
- obj.cells.categories[obj.use_category_index].hidden_types.push(type);
1049
- }
1050
- pcd_pipeline(obj);
1051
- }
1052
- });
1053
- if (obj.cells.categories[obj.use_category_index].hidden_types.length == 0) {
1054
- select_all_checkbox.property("checked", 1);
1055
- }
1056
- top_row.append("span").text("Select All").style("font-size", ".8em").attr("font-family", font);
1057
- for (const type in data.category2color) {
1058
- const row = obj.menu_output.append("div").style("margin", "2px");
1059
- 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", () => {
1060
- if (obj.cells.categories[obj.use_category_index].hidden_types.includes(type)) {
1061
- const index = obj.cells.categories[obj.use_category_index].hidden_types.indexOf(type);
1062
- if (index !== -1) obj.cells.categories[obj.use_category_index].hidden_types.splice(index, 1);
1063
- checkbox.property("checked", 1);
1064
- } else {
1065
- obj.cells.categories[obj.use_category_index].hidden_types.push(type);
1066
- }
1067
- pcd_pipeline(obj);
1068
- });
1069
- if (obj.cells.categories[obj.use_category_index].hidden_types.includes(type)) {
1070
- checkbox.property("checked", 0);
1071
- }
1072
- row.append("div").style("display", "inline-block").style("height", "15px").style("width", "15px").style("background-color", data.category2color[type]).style("margin-right", "10px");
1073
- row.append("span").text(type).attr("font-family", font);
1074
- row.append("span").html("&nbsp;n=" + data.categorycount[type]).attr("font-family", font).style("font-size", ".8em").style("float", "right").style("color", "#777");
1075
- }
1076
- } else if (data.maxexpvalue) {
1077
- const scale_height = 30;
1078
- const scale_width = 150;
1079
- const scale_div = obj.menu_output.append("div").style("margin", "10px").style("width", "120px").style("height", "100px");
1080
- scale_div.append("div").text("Gene Expression " + obj.gene_expression.datatype).style("text-align", "center").style("width", "150px").style("margin-bottom", "20px");
1081
- const svg = scale_div.append("svg").append("g");
1082
- const colorRange = [obj.gene_expression.color_max, obj.gene_expression.color_min];
1083
- const colorScale = linear().range(colorRange).domain([data.minexpvalue, data.maxexpvalue]);
1084
- const defs = svg.append("defs");
1085
- const linearGradient = defs.append("linearGradient").attr("id", "linear-gradient");
1086
- linearGradient.append("stop").attr("offset", "0%").attr("stop-color", colorScale(data.maxexpvalue));
1087
- linearGradient.append("stop").attr("offset", "100%").attr("stop-color", colorScale(data.minexpvalue));
1088
- 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)");
1089
- const y = linear().range([0, scale_width]).domain([data.minexpvalue, data.maxexpvalue]);
1090
- const legendAxis = axisBottom().scale(y).ticks(5);
1091
- svg.append("g").attr("class", "legend axis").attr("transform", "translate(12," + scale_height + ")").call(legendAxis);
1092
- const stats_div = obj.menu_output.append("div").style("padding-bottom", "20px").style("text-align", "center");
1093
- stats_div.append("p").style("font-size", "13px").style("margin", "2px 0").html("<b>Cells with Expression Data</b> ");
1094
- stats_div.append("p").style("font-size", "13px").style("margin", "2px 0").html(data.numbercellwithgeneexp + " / " + data.numbercelltotal);
1095
- const no_exp_div = stats_div.append("div").style("display", "block").style("margin-top", "10px");
1096
- 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");
1097
- no_exp_div.append("div").style("display", "inline-block").style("font-size", "13px").html(" Cells without Expression");
1098
- const boxplot_div = obj.menu_output.append("div");
1099
- boxplot_div.append("div").style("display", "block").style("padding", "5px").html("Violinplot / Boxplot of </br> Expression by");
1100
- const boxplot_cat_select = boxplot_div.append("select").style("display", "block");
1101
- boxplot_cat_select.append("option").attr("value", "none").text("-- Select--");
1102
- if (obj.cells.categories) {
1103
- obj.cells.categories.forEach((category, i) => {
1104
- boxplot_cat_select.append("option").attr("value", category.columnidx).text(category.name);
1105
- });
1106
- }
1107
- boxplot_cat_select.on("change", () => {
1108
- const gene = obj.gene_expression.genes[obj.use_gene_index];
1109
- const cat = obj.cells.categories[parseInt(boxplot_cat_select.node().selectedIndex) - 1];
1110
- const arg = {
1111
- genome: obj.genome.name,
1112
- getgeneboxplot: {
1113
- expfile: obj.gene_expression.file,
1114
- chr: gene.chr,
1115
- start: gene.start,
1116
- stop: gene.stop,
1117
- genename: gene.gene,
1118
- cellfile: obj.cells.file,
1119
- barcodecolumnidx: obj.cells.barcodecolumnidx,
1120
- categorycolumnidx: parseInt(boxplot_cat_select.node().value),
1121
- delimiter: obj.cells.delimiter || " ",
1122
- category_customorder: cat.customorder && cat.values ? true : false,
1123
- category_autoorder: !cat.customorder ? true : false,
1124
- cat_values: cat.values,
1125
- values_count: cat.values_count
1126
- }
1127
- };
1128
- dofetch("singlecell", arg).then((data2) => {
1129
- if (data2.error) throw data2.error;
1130
- obj.box_plot = new Menu();
1131
- make_plot(data2, obj, boxplot_cat_select.node().value);
1132
- });
1133
- });
1134
- }
1135
- make_zoom_panel(obj);
1136
- }
1137
- function make_zoom_panel(obj) {
1138
- if (obj.show_zoom) {
1139
- 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");
1140
- 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", () => {
1141
- zoom_div.node().remove();
1142
- obj.show_zoom = false;
1143
- }).on("mouseover", () => {
1144
- zoom_hide_btn.style("text-decoration", "underline");
1145
- }).on("mouseout", () => {
1146
- zoom_hide_btn.style("text-decoration", "none");
1147
- });
1148
- 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", () => {
1149
- obj.camera.fov = parseInt(obj.zoom_slider.node().value);
1150
- obj.camera.updateProjectionMatrix();
1151
- }).on("mousedown", (event) => {
1152
- event.stopPropagation();
1153
- });
1154
- }
1155
- }
1156
- function make_menu(obj) {
1157
- obj.menu.clear().showunder(obj.menu_button.node());
1158
- if (obj.cells.categories) {
1159
- obj.cells.categories.forEach((category, i) => {
1160
- if (i != obj.use_category_index) {
1161
- obj.menu.d.append("div").text(category.name).attr("class", "sja_menuoption").on("click", async () => {
1162
- obj.menu.hide();
1163
- obj.use_category_index = i;
1164
- pcd_pipeline(obj);
1165
- }).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 : "");
1166
- }
1167
- });
1168
- }
1169
- if (obj.gene_expression) {
1170
- obj.menu.d.append("div").text("Gene expression").attr("class", "sja_menuoption").on("click", () => {
1171
- obj.menu.clear();
1172
- const gene_search_div = obj.menu.d.append("div").style("padding", "10px");
1173
- gene_searchbox({
1174
- div: gene_search_div.append("div"),
1175
- resultdiv: gene_search_div.append("div"),
1176
- genome: obj.genome.name,
1177
- callback: async (genename) => {
1178
- const gmlst = await findgenemodel_bysymbol(obj.genome.name, genename);
1179
- if (gmlst && gmlst[0]) {
1180
- const gm = gmlst[0];
1181
- if (!obj.gene_expression.genes) obj.gene_expression.genes = [];
1182
- const geneidx = obj.gene_expression.genes.findIndex((i) => i.gene == genename);
1183
- if (geneidx == -1) {
1184
- obj.gene_expression.genes.push({
1185
- gene: genename,
1186
- chr: gm.chr,
1187
- start: gm.start,
1188
- stop: gm.stop
1189
- });
1190
- obj.use_gene_index = obj.gene_expression.genes.length - 1;
1191
- } else {
1192
- obj.use_gene_index = geneidx;
1193
- }
1194
- }
1195
- obj.use_category_index = null;
1196
- obj.menu.hide();
1197
- pcd_pipeline(obj);
1198
- }
1199
- });
1200
- });
1201
- obj.menu.d.append("div").text("Multi-Gene Heatmap").attr("class", "sja_menuoption").on("click", () => {
1202
- heatmap_menu(obj);
1203
- });
1204
- if (obj.gene_expression.genes) {
1205
- if (obj.gene_expression.genes.length > 1) {
1206
- obj.menu.d.append("div").style("padding", "5px 10px").text("Previously Selected");
1207
- }
1208
- obj.gene_expression.genes.forEach((gene, i) => {
1209
- if (i != obj.use_gene_index) {
1210
- obj.menu.d.append("div").text("Gene : " + gene.gene).attr("class", "sja_menuoption").on("click", async () => {
1211
- obj.menu.hide();
1212
- obj.use_category_index = null;
1213
- obj.use_gene_index = i;
1214
- pcd_pipeline(obj);
1215
- });
1216
- }
1217
- });
1218
- }
1219
- }
1220
- }
1221
- function make_settings(obj) {
1222
- obj.settings.clear().showunder(obj.settings_btn.node());
1223
- const back_color_div = obj.settings.d.append("div").style("display", "block").text("Background Color").style("margin", "5px");
1224
- const black_div = back_color_div.append("div").style("margin", "5px").style("display", "block");
1225
- const name = Math.random(), idblack = Math.random(), idwhite = Math.random();
1226
- const inputblack = black_div.append("input").attr("type", "radio").style("display", "inline-block").attr("name", name).attr("id", idblack).on("change", toggle_background);
1227
- black_div.append("label").style("display", "inline-block").style("font-size", ".8em").text("Black").style("padding-left", "10px").attr("for", idblack);
1228
- const white_div = back_color_div.append("div").style("margin", "5px").style("display", "block");
1229
- const inputwhite = white_div.append("input").attr("type", "radio").style("display", "inline-block").attr("name", name).attr("id", idwhite).on("change", toggle_background);
1230
- white_div.append("label").style("display", "inline-block").style("font-size", ".8em").text("White").style("padding-left", "10px").attr("for", idwhite);
1231
- if (obj.use_background_color == 0) {
1232
- inputwhite.property("checked", 1);
1233
- } else {
1234
- inputblack.property("checked", 1);
1235
- }
1236
- function toggle_background() {
1237
- const isblack = obj.background_color == "black";
1238
- obj.scene.background = new Color(isblack ? 16777215 : 0);
1239
- obj.use_background_color = isblack ? 0 : 1;
1240
- obj.background_color = isblack ? "white" : "black";
1241
- }
1242
- const point_size_div = obj.settings.d.append("div").style("display", "block").text("Point Size").style("margin", "20px 5px");
1243
- 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", () => {
1244
- obj.scene.children[1].material.size = point_size_slider.node().value / 100;
1245
- });
1246
- if (obj.show_zoom == false) {
1247
- const zoom_div = obj.settings.d.append("div").style("display", "block").text("Zoom").style("margin", "20px 5px");
1248
- 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", () => {
1249
- zoom_div.node().remove();
1250
- obj.show_zoom = true;
1251
- make_zoom_panel(obj);
1252
- }).on("mouseover", () => {
1253
- zoom_hide_btn.style("text-decoration", "underline");
1254
- }).on("mouseout", () => {
1255
- zoom_hide_btn.style("text-decoration", "none");
1256
- });
1257
- 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", () => {
1258
- obj.camera.fov = parseInt(obj.zoom_slider.node().value);
1259
- obj.camera.updateProjectionMatrix();
1260
- });
1261
- }
1262
- obj.settings.d.append("div").style("margin", "5px").text("Panning");
1263
- 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>');
1264
- if (!obj.canvas_2d) {
1265
- obj.settings.d.append("div").style("margin", "5px").text("Rotate");
1266
- 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>');
1267
- }
1268
- 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", () => {
1269
- inputwhite.property("checked", 1);
1270
- obj.scene.background = new Color(obj.background_color ? obj.background_color : 16777215);
1271
- point_size_slider.node().value = obj.point_size ? obj.point_size * 100 : obj.canvas_2d ? 30 : 5;
1272
- obj.scene.children[1].material.size = obj.point_size ? obj.point_size : obj.canvas_2d ? 0.3 : 0.05;
1273
- obj.camera.position.z = obj.data_sphere_r * 3;
1274
- obj.camera.position.x = obj.canvas_2d ? 0 : 20;
1275
- obj.camera.position.y = obj.canvas_2d ? 0 : -10;
1276
- const cam_fov_default = 45;
1277
- obj.camera.fov = parseInt(cam_fov_default);
1278
- obj.camera.updateProjectionMatrix();
1279
- obj.zoom_slider.node().value = cam_fov_default;
1280
- if (obj.canvas_2d) {
1281
- obj.camera.up.set(0, 1, 0);
1282
- } else {
1283
- obj.camera.up.set(0, 0, 1);
1284
- }
1285
- obj.controls.target.set(obj.center.x, obj.center.y, obj.center.z);
1286
- });
1287
- 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", () => {
1288
- const imgData = obj.renderer.domElement.toDataURL();
1289
- let imgNode = document.createElement("img");
1290
- imgNode.src = imgData;
1291
- screenshot_btn.append("span").style("display", "none").html(
1292
- '<a download="scRNA_' + (/* @__PURE__ */ new Date()).toLocaleString() + '.png" href="' + imgNode.src + '" title="ImageName">Camera</a>'
1293
- );
1294
- }).on("mouseup", () => {
1295
- screenshot_btn.select("a").node().click();
1296
- screenshot_btn.selectAll("span").remove();
1297
- });
1298
- }
1299
- function heatmap_menu(obj) {
1300
- obj.menu.clear();
1301
- obj.gene_expression.heatmap_genes = [];
1302
- obj.use_heatmap_category_index = null;
1303
- const heatmap_menu_div = obj.menu.d.append("div").style("display", "block").style("padding", "10px");
1304
- const genes_div = heatmap_menu_div.append("div").style("display", "block");
1305
- const gene_search_div = genes_div.append("div").style("display", "inline-block").style("vertical-align", "top").style("padding", "10px");
1306
- gene_search_div.append("div").style("display", "block").style("padding-bottom", "5px").text("Add Genes");
1307
- gene_search_div.append("textarea").attr("rows", "4").attr("cols", "20").attr("placeholder", "Type gene names seperated by space");
1308
- const catagory_div = heatmap_menu_div.append("div");
1309
- catagory_div.append("div").style("display", "block").style("padding-bottom", "5px").style("padding-left", "10px").text("Heatmap by");
1310
- const cat_select = catagory_div.append("select").style("display", "block").style("margin-left", "10px");
1311
- cat_select.append("option").attr("value", "none").text("-- Select--");
1312
- if (obj.cells.categories) {
1313
- obj.cells.categories.forEach((category, i) => {
1314
- cat_select.append("option").attr("value", category.columnidx).text(category.name);
1315
- });
1316
- }
1317
- cat_select.on("change", () => {
1318
- obj.use_heatmap_category_index = parseInt(cat_select.node().value);
1319
- });
1320
- heatmap_menu_div.append("button").text("Heatmap").style("display", "block").style("float", "right").style("margin", "5px").on("click", async () => {
1321
- const input_genelist = gene_search_div.select("textarea").node().value;
1322
- const genelist = input_genelist.split(" ");
1323
- for (const gene of genelist) {
1324
- const gmlst = await findgenemodel_bysymbol(obj.genome.name, gene);
1325
- if (gmlst && gmlst[0]) {
1326
- const gm = gmlst[0];
1327
- if (!obj.gene_expression.heatmap_genes) obj.gene_expression.heatmap_genes = [];
1328
- const geneidx = obj.gene_expression.heatmap_genes.findIndex((i) => i.gene == gene);
1329
- if (geneidx == -1) {
1330
- obj.gene_expression.heatmap_genes.push({
1331
- gene,
1332
- chr: gm.chr,
1333
- start: gm.start,
1334
- stop: gm.stop
1335
- });
1336
- }
1337
- }
1338
- }
1339
- const arg = {
1340
- genome: obj.genome.name,
1341
- getheatmap: {
1342
- expfile: obj.gene_expression.file,
1343
- gene_list: obj.gene_expression.heatmap_genes,
1344
- cellfile: obj.cells.file,
1345
- barcodecolumnidx: obj.cells.barcodecolumnidx,
1346
- categorycolumnidx: parseInt(cat_select.node().value),
1347
- delimiter: obj.cells.delimiter || " "
1348
- }
1349
- };
1350
- dofetch("singlecell", arg).then((data) => {
1351
- if (data.error) throw data.error;
1352
- obj.menu.hide();
1353
- make_heatmap(data, obj, cat_select.node().value);
1354
- });
1355
- });
1356
- }
1357
- function make_plot(data, obj, colidx) {
1358
- const gene = obj.gene_expression.genes[obj.use_gene_index];
1359
- const pane = newpane({ x: 600, y: 400 });
1360
- const cat = obj.cells.categories.find((x) => x.columnidx == colidx);
1361
- pane.header.text("Violinplot/Boxplot for " + gene.gene + " Expression by " + cat.name);
1362
- const control_panel = pane.pane.append("div").style("margin", "10px 10px 10px 15px");
1363
- const svg = pane.pane.append("svg").style("margin", "10px");
1364
- const plot_select = control_panel.append("select").style("display", "inline-block");
1365
- plot_select.append("option").attr("value", "violin").text("Violin Plot");
1366
- plot_select.append("option").attr("value", "box").text("Box Plot");
1367
- plot_select.on("change", () => {
1368
- apply();
1369
- });
1370
- const cell_select_div = control_panel.append("div").style("display", "inline-block").style("padding-left", "15px").text("Cells without expression");
1371
- const cell_select = cell_select_div.append("select").style("display", "inline-block").style("margin-left", "5px");
1372
- cell_select.append("option").attr("value", "include").text("Include");
1373
- cell_select.append("option").attr("value", "exclude").text("Exclude");
1374
- cell_select.on("change", () => {
1375
- apply();
1376
- });
1377
- make_violin_plot(data, svg);
1378
- function apply() {
1379
- const gene2 = obj.gene_expression.genes[obj.use_gene_index];
1380
- const arg = {
1381
- genome: obj.genome.name,
1382
- getgeneboxplot: {
1383
- expfile: obj.gene_expression.file,
1384
- chr: gene2.chr,
1385
- start: gene2.start,
1386
- stop: gene2.stop,
1387
- genename: gene2.gene,
1388
- cellfile: obj.cells.file,
1389
- barcodecolumnidx: obj.cells.barcodecolumnidx,
1390
- categorycolumnidx: parseInt(colidx),
1391
- delimiter: obj.cells.delimiter || " ",
1392
- category_customorder: cat.customorder && cat.values ? true : false,
1393
- category_autoorder: !cat.customorder ? true : false,
1394
- cat_values: cat.values,
1395
- values_count: cat.values_count
1396
- }
1397
- };
1398
- if (cell_select.node().value == "exclude") {
1399
- arg.getgeneboxplot.exclude_cells = true;
1400
- }
1401
- dofetch("singlecell", arg).then((data2) => {
1402
- if (data2.error) throw data2.error;
1403
- if (plot_select.node().value == "box") make_box_plot(data2, svg);
1404
- else if (plot_select.node().value == "violin") make_violin_plot(data2, svg);
1405
- });
1406
- }
1407
- }
1408
- function make_violin_plot(data, svg) {
1409
- svg.selectAll("*").remove();
1410
- let box_height = 50, box_width = 200, barspace = 2, axis_height = 30;
1411
- const label_width = get_max_labelwidth(data.boxplots, svg);
1412
- const x_scale = linear().range([0, box_width]).domain([data.minexpvalue, data.maxexpvalue]);
1413
- const y_scale = linear().range([box_height, 0]).domain([0, 1]);
1414
- const svg_height = data.boxplots.length * (box_height + barspace) + axis_height;
1415
- const svg_width = box_width + label_width + 20;
1416
- svg.transition().attr("width", svg_width).attr("height", svg_height);
1417
- if (data.boxplots) {
1418
- data.boxplots.forEach((boxplot, i) => {
1419
- const g = svg.append("g").attr("transform", "translate(" + label_width + "," + (i * (box_height + barspace) + axis_height) + ")");
1420
- 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");
1421
- if (boxplot.density) {
1422
- const density_max = Math.max(...boxplot.density);
1423
- const line = line_default().x(function(d, j) {
1424
- return x_scale(j * data.maxexpvalue / boxplot.density.length);
1425
- }).y(function(d) {
1426
- return y_scale(d / density_max) / 2;
1427
- }).curve(monotoneX);
1428
- const area = area_default().x(function(d, j) {
1429
- return x_scale(j * data.maxexpvalue / boxplot.density.length);
1430
- }).y0(function(d) {
1431
- const temp = y_scale(d / density_max) / 2;
1432
- return box_height - temp;
1433
- }).y1(function(d) {
1434
- return y_scale(d / density_max) / 2;
1435
- }).curve(monotoneX);
1436
- g.append("path").datum(boxplot.density).attr("class", "area").attr("d", area).style("fill", boxplot.color).style("stroke", "black").style("stroke-width", 0.5);
1437
- }
1438
- });
1439
- const legendAxis = axisTop().scale(x_scale).ticks(5);
1440
- svg.append("g").attr("class", "legend axis").attr("transform", "translate(" + label_width + "," + (axis_height - 10) + ")").call(legendAxis);
1441
- }
1442
- }
1443
- function make_box_plot(data, svg) {
1444
- svg.selectAll("*").remove();
1445
- let box_height = 36, box_width = 200, barspace = 16, axis_height = 30;
1446
- const label_width = get_max_labelwidth(data.boxplots, svg);
1447
- const x_scale = linear().range([0, box_width]).domain([data.minexpvalue, data.maxexpvalue]);
1448
- const y_scale = linear().range([box_height, 0]).domain([0, 1]);
1449
- const svg_height = data.boxplots.length * (box_height + barspace) + axis_height;
1450
- const svg_width = box_width + label_width + 20;
1451
- svg.transition().attr("width", svg_width).attr("height", svg_height);
1452
- if (data.boxplots) {
1453
- data.boxplots.forEach((boxplot, i) => {
1454
- const g = svg.append("g").attr("transform", "translate(" + label_width + "," + (i * (box_height + barspace) + axis_height) + ")");
1455
- 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");
1456
- if (boxplot.p75) {
1457
- 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");
1458
- 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);
1459
- 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");
1460
- 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");
1461
- 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");
1462
- if (boxplot.out) {
1463
- for (const outlier of boxplot.out) {
1464
- g.append("circle").attr("cx", x_scale(outlier.value)).attr("cy", box_height / 2).attr("r", 2).attr("fill", "#901739");
1465
- }
1466
- }
1467
- }
1468
- });
1469
- const legendAxis = axisTop().scale(x_scale).ticks(5);
1470
- svg.append("g").attr("class", "legend axis").attr("transform", "translate(" + label_width + "," + (axis_height - 10) + ")").call(legendAxis);
1471
- }
1472
- }
1473
- function make_heatmap(data, obj, colidx) {
1474
- const pane = newpane({ x: 600, y: 400 });
1475
- const cat = obj.cells.categories.find((x) => x.columnidx == colidx);
1476
- pane.header.text("Heatmap for Gene Expression by " + cat.name);
1477
- const svg = pane.pane.append("svg").style("margin", "10px");
1478
- let gene_list = [];
1479
- for (const gene of data.gene_heatmap) gene_list.push(gene.genename);
1480
- let means = [];
1481
- data.gene_heatmap.forEach((gene, i) => {
1482
- data.gene_heatmap[i].heatmap.forEach((category) => {
1483
- means.push(category.mean);
1484
- });
1485
- });
1486
- const max_mean = Math.max(...means);
1487
- let categories = [];
1488
- for (const category of data.gene_heatmap[0].heatmap)
1489
- categories.push(category.category + " (" + category.numberofcells + ")");
1490
- let box_height = 20, box_width = 80, barspace = 2, gene_lable_height = 30, legend_width = 60;
1491
- const label_width = get_max_labelwidth(data.gene_heatmap[0].heatmap, svg);
1492
- const svg_height = (box_height + barspace) * categories.length + gene_lable_height;
1493
- const svg_width = (box_width + barspace) * gene_list.length + label_width + legend_width + 20;
1494
- svg.transition().attr("width", svg_width).attr("height", svg_height);
1495
- const x_scale = band().range([0, (box_width + barspace) * gene_list.length]).domain(gene_list).padding(0.05);
1496
- svg.append("g").style("font-size", 15).attr("transform", "translate(" + label_width + ",0)").call(axisBottom(x_scale).tickSize(0)).select(".domain").remove();
1497
- const y_scale = band().range([(box_height + barspace) * categories.length, 0]).domain(categories).padding(0.05);
1498
- svg.append("g").style("font-size", 15).attr("transform", "translate(" + label_width + "," + gene_lable_height + ")").call(axisLeft(y_scale).tickSize(0)).select(".domain").remove();
1499
- var myColor = sequential().interpolator(plasma).domain([0, max_mean]);
1500
- 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);
1501
- data.gene_heatmap.forEach((gene, i) => {
1502
- data.gene_heatmap[i].heatmap.forEach((category, j) => {
1503
- const g = svg.append("g").attr("transform", "translate(" + label_width + "," + gene_lable_height + ")");
1504
- 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) {
1505
- div.transition().duration(200).style("opacity", 0.9);
1506
- div.html("Mean Expression: " + category.mean).style("left", pointer_default(event, this)[0] + 70 + "px").style("top", pointer_default(event, this)[1] + 20 + "px");
1507
- }).on("mouseout", function() {
1508
- div.transition().duration(500).style("opacity", 0);
1509
- });
1510
- });
1511
- });
1512
- const legend_data = myColor.ticks(10).reverse();
1513
- legend_data.unshift(max_mean.toFixed(2));
1514
- const legend = svg.selectAll(".legend").data(legend_data).enter().append("g").attr("class", "legend").attr("transform", function(d, i) {
1515
- return "translate(" + (svg_width - legend_width) + "," + (30 + i * 20) + ")";
1516
- });
1517
- legend.append("rect").attr("width", 20).attr("height", 20).style("fill", myColor).style("opacity", 0.8);
1518
- legend.append("text").attr("x", 26).attr("y", 10).attr("dy", ".35em").text(String);
1519
- }
1520
- function get_max_labelwidth(items, svg) {
1521
- let textwidth = 0;
1522
- for (const i of items) {
1523
- svg.append("text").text(i.category + " (" + i.numberofcells + ")").attr("font-family", font).attr("font-size", 15).each(function() {
1524
- textwidth = Math.max(textwidth, this.getBBox().width);
1525
- }).remove();
1526
- }
1527
- return textwidth + 4;
1528
- }
1529
- async function make_legend(arg, obj) {
1530
- if (!arg.legendimg) return;
1531
- const img_div = obj.holder.append("div").style("margin-top", "5px");
1532
- obj.legendimg = arg.legendimg;
1533
- obj.legend = {
1534
- holder: img_div,
1535
- legendcolor: "#7D6836"
1536
- };
1537
- let shown = !arg.foldlegend;
1538
- 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", () => {
1539
- if (shown) {
1540
- shown = false;
1541
- disappear(div2);
1542
- } else {
1543
- shown = true;
1544
- appear(div2);
1545
- }
1546
- });
1547
- const div2 = obj.holder.append("div").style("border-top", "solid 1px " + obj.legend.legendcolor).style("background-color", "#FCFBF7");
1548
- obj.legend.holder = div2.append("table").style("border-spacing", "15px").style("border-collapse", "separate");
1549
- const [tr, td] = legend_newrow(obj, obj.legendimg.name || "");
1550
- const data = await dofetch2("img?file=" + obj.legendimg.file);
1551
- if (data.error) {
1552
- td.text(data.error);
1553
- return;
1554
- }
1555
- let fold = true;
1556
- const img = td.append("img").attr("class", "sja_clbb").attr("src", data.src).style("height", "80px");
1557
- img.on("click", () => {
1558
- if (fold) {
1559
- fold = false;
1560
- img.transition().style("height", obj.legendimg.height ? obj.legendimg.height + "px" : "auto");
1561
- } else {
1562
- fold = true;
1563
- img.transition().style("height", "80px");
1564
- }
1565
- });
1566
- }
1567
- export {
1568
- init
1569
- };
1570
- //# sourceMappingURL=singlecell-HL4GLGIA.js.map