@sjcrh/proteinpaint-client 2.210.0 → 2.210.1

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 (915) hide show
  1. package/dist/2dmaf-7VZ536T5.js +1367 -0
  2. package/dist/AggMatrixInput-UTUOXTGA.js +406 -0
  3. package/dist/AggregateMatrix-X75HUZYO.js +41 -0
  4. package/dist/AppHeader-X2DR6VSM.js +830 -0
  5. package/dist/BoxPlot-NQMPJICU.js +1211 -0
  6. package/dist/CorrelationVolcano-IDBUJH2E.js +617 -0
  7. package/dist/Cuminc-BYFIMOLO.js +1219 -0
  8. package/dist/DE-BI7DHHW4.js +89 -0
  9. package/dist/DEinput-W66CT4U2.js +501 -0
  10. package/dist/DM-62TEJA3C.js +90 -0
  11. package/dist/DifferentialAnalysis-PRTA6CYW.js +239 -0
  12. package/dist/Disco-4JQP3FRW.js +3389 -0
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  14. package/dist/DmrPlot-VYQYMTQ7.js +362 -0
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  17. package/dist/GSEA-DT3SYXOZ.js +875 -0
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  161. package/dist/databrowser.ui-L2K7VVDW.js +425 -0
  162. package/dist/dictionary-MS6R3VNY.js +113 -0
  163. package/dist/dnaMethylation-2KYSQWNE.js +33 -0
  164. package/dist/dnaMethylation.integration.spec-2BHNKOGN.js +198 -0
  165. package/dist/dofetch-BETN7HEX.js +48 -0
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  167. package/dist/ep-BTRMR4OT.js +1249 -0
  168. package/dist/expclust.gdc.spec-C5ZMBCGO.js +302 -0
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  171. package/dist/geneExpClustering-OXZJHEPD.js +244 -0
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  177. package/dist/geneVariant-NJYUEY4C.js +36 -0
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  180. package/dist/genefusion.ui-B6J7I3RA.js +303 -0
  181. package/dist/geneset-VG4SFYML.js +203 -0
  182. package/dist/genomeBrowser.spec-5IS5Y2NG.js +276 -0
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  827. /package/dist/{mavb-GWSNRBLM.js.map → mavb-3CL5OHWB.js.map} +0 -0
  828. /package/dist/{mds.fimo-OMAQRSMW.js.map → mds.fimo-2RFJQKJM.js.map} +0 -0
  829. /package/dist/{mds.samplescatterplot-4UW3CC45.js.map → mds.samplescatterplot-X6CXMY4C.js.map} +0 -0
  830. /package/dist/{mds.survivalplot-2CJYJBD2.js.map → mds.survivalplot-57NIKSSH.js.map} +0 -0
  831. /package/dist/{multivalue-G44MHEYI.js.map → multivalue-3TUGYL4J.js.map} +0 -0
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  834. /package/dist/{oncomatrix.spec-2QVK2A3Q.js.map → oncomatrix.spec-SO3ZN5BF.js.map} +0 -0
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  843. /package/dist/{polar2-TMB5EITR.js.map → polar2-AVEZM2T5.js.map} +0 -0
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  845. /package/dist/{profilePlot-CZLK5E74.js.map → profilePlot-67Z7AXQ4.js.map} +0 -0
  846. /package/dist/{proteinView-FEEEXLKT.js.map → proteinView-7K7VHGX3.js.map} +0 -0
  847. /package/dist/{proteomeCohortCompare-NVLJ2FXX.js.map → proteomeCohortCompare-MRGH6HHI.js.map} +0 -0
  848. /package/dist/{pseudbulk.unit.spec-GHQZPNAH.js.map → pseudbulk.unit.spec-ZHDL6GIM.js.map} +0 -0
  849. /package/dist/{pseudobulk-G5UQIRKL.js.map → pseudobulk-ZNXPF7QB.js.map} +0 -0
  850. /package/dist/{qualitative-EAUUCKU5.js.map → qualitative-QXMZHDWU.js.map} +0 -0
  851. /package/dist/{radar2-CJQ2L6KE.js.map → radar2-QJDGNLED.js.map} +0 -0
  852. /package/dist/{radarFacility2-BLVRZE4V.js.map → radarFacility2-LGGOOWX4.js.map} +0 -0
  853. /package/dist/{rememberedGvQ.unit.spec-DYRO2LO5.js.map → rememberedGvQ.unit.spec-YKUMMYFT.js.map} +0 -0
  854. /package/dist/{render-KKAQPH6Y.js.map → render-LSSRZJY3.js.map} +0 -0
  855. /package/dist/{report-OSOJHTSD.js.map → report-TTECPO44.js.map} +0 -0
  856. /package/dist/{sampleView-WB74RLD7.js.map → sampleView-EFS2UBRS.js.map} +0 -0
  857. /package/dist/{samplelst-ZKXV5WOD.js.map → samplelst-FXULLJBO.js.map} +0 -0
  858. /package/dist/{samplematrix-WJFYMWLT.js.map → samplematrix-MNFCXOWO.js.map} +0 -0
  859. /package/dist/{sc-RBRBUCLR.js.map → sc-2BUOXML2.js.map} +0 -0
  860. /package/dist/{scatter-SM7GQENM.js.map → scatter-AVRTALYY.js.map} +0 -0
  861. /package/dist/{scatter-5K3QTIDK.js.map → scatter-CPEIVL3K.js.map} +0 -0
  862. /package/dist/{selectGenomeWithTklst-ZZUJ7AQ7.js.map → selectGenomeWithTklst-3BG2ZPPN.js.map} +0 -0
  863. /package/dist/{singleCellCellType-LCF2JNZ2.js.map → singleCellCellType-QLAEBVN2.js.map} +0 -0
  864. /package/dist/{singleCellCellType.unit.spec-T6DYH4BC.js.map → singleCellCellType.unit.spec-P4NAWYKL.js.map} +0 -0
  865. /package/dist/{singleCellGeneExpression-2XUYTH4C.js.map → singleCellGeneExpression-IZ2PMDDL.js.map} +0 -0
  866. /package/dist/{singleCellGeneExpression.unit.spec-SMRCLOF4.js.map → singleCellGeneExpression.unit.spec-DKBZICJM.js.map} +0 -0
  867. /package/dist/{singleCellNumericValue-57I33FZT.js.map → singleCellNumericValue-NB3QFH7H.js.map} +0 -0
  868. /package/dist/{singleCellNumericValue.unit.spec-4YNB4OEV.js.map → singleCellNumericValue.unit.spec-ZKK2KWRQ.js.map} +0 -0
  869. /package/dist/{singleCellPlot-L6TKQHGD.js.map → singleCellPlot-ZU655L4Z.js.map} +0 -0
  870. /package/dist/{singlecell-UKN2VCXQ.js.map → singlecell-NKPTXVHW.js.map} +0 -0
  871. /package/dist/{singlecell-LZKR3UDV.js.map → singlecell-PEIEFXVU.js.map} +0 -0
  872. /package/dist/{snp-3LJITU5B.js.map → snp-G55JGINX.js.map} +0 -0
  873. /package/dist/{snp.unit.spec-ZQNU6XRM.js.map → snp.unit.spec-47CCZKJO.js.map} +0 -0
  874. /package/dist/{snplocus-OME7UQBW.js.map → snplocus-TRVAEAPF.js.map} +0 -0
  875. /package/dist/{spliceevent.a53ss.diagram-C32IEFMU.js.map → spliceevent.a53ss.diagram-FL2R6F22.js.map} +0 -0
  876. /package/dist/{spliceevent.exonskip.diagram-CZ7MVRLK.js.map → spliceevent.exonskip.diagram-XDZWTJXR.js.map} +0 -0
  877. /package/dist/{spliceevent.noeventdiagram-ZO6R3776.js.map → spliceevent.noeventdiagram-L322N534.js.map} +0 -0
  878. /package/dist/{ssGSEA-BGPQ2PFY.js.map → ssGSEA-DZY4LFQY.js.map} +0 -0
  879. /package/dist/{ssGSEA.unit.spec-U7TBUSSK.js.map → ssGSEA.unit.spec-P6C3VTVZ.js.map} +0 -0
  880. /package/dist/{stattable-FISGQCED.js.map → stattable-R7O6OIMB.js.map} +0 -0
  881. /package/dist/{studyCatalog-UHFUT2CJ.js.map → studyCatalog-OMDE4JRD.js.map} +0 -0
  882. /package/dist/{summarizeCnvGeneexp-OVZO6KIB.js.map → summarizeCnvGeneexp-A7HW6FJI.js.map} +0 -0
  883. /package/dist/{summarizeGeneexpSurvival-KVQ4JGWK.js.map → summarizeGeneexpSurvival-ODI4HGFH.js.map} +0 -0
  884. /package/dist/{summarizeMutationCnv-RAKGHNLE.js.map → summarizeMutationCnv-C2YB73OL.js.map} +0 -0
  885. /package/dist/{summarizeMutationDiagnosis-LGCINAGG.js.map → summarizeMutationDiagnosis-4Y322NYU.js.map} +0 -0
  886. /package/dist/{summarizeMutationSurvival-J7H7L4FX.js.map → summarizeMutationSurvival-7IHNURLC.js.map} +0 -0
  887. /package/dist/{summary-2632JZXH.js.map → summary-E4L5MZTF.js.map} +0 -0
  888. /package/dist/{summary.integration.spec-5WBS2ZRP.js.map → summary.integration.spec-SDCGE6BQ.js.map} +0 -0
  889. /package/dist/{summaryInput-BH6C3ATV.js.map → summaryInput-DHIMU5DM.js.map} +0 -0
  890. /package/dist/{sunburst-AMRR2IHM.js.map → sunburst-ULNPFEAM.js.map} +0 -0
  891. /package/dist/{survival-WYCH4QOQ.js.map → survival-CU4N5KZO.js.map} +0 -0
  892. /package/dist/{survival-2RNJQVFS.js.map → survival-KWWH6REE.js.map} +0 -0
  893. /package/dist/{survival.integration.spec-7IFPY4I4.js.map → survival.integration.spec-UW6SYVLP.js.map} +0 -0
  894. /package/dist/{svgraph-YQWS52ZJ.js.map → svgraph-HFI6NNF3.js.map} +0 -0
  895. /package/dist/{svmr-NRN6LGKK.js.map → svmr-VHS7Z4SO.js.map} +0 -0
  896. /package/dist/{table-3QOMV2NN.js.map → table-GJUXHKQI.js.map} +0 -0
  897. /package/dist/{termCollection-2ZJ7TJGO.js.map → termCollection-CCZ4BFIU.js.map} +0 -0
  898. /package/dist/{termCollection-3MCVR7BA.js.map → termCollection-O5CQ472U.js.map} +0 -0
  899. /package/dist/{termCollection.unit.spec-QYOEA3X6.js.map → termCollection.unit.spec-KR5G6JFU.js.map} +0 -0
  900. /package/dist/{termCollectionFractionSelection-5AH6EF4L.js.map → termCollectionFractionSelection-IKU5MFBT.js.map} +0 -0
  901. /package/dist/{termCollectionFractionSelection.unit.spec-WPGW4WJN.js.map → termCollectionFractionSelection.unit.spec-6ZWHNGES.js.map} +0 -0
  902. /package/dist/{tk-DQ7D5UEO.js.map → tk-3DLMAFW7.js.map} +0 -0
  903. /package/dist/{tk-ONKYBG6R.js.map → tk-CAYWF7LX.js.map} +0 -0
  904. /package/dist/{tp.ui-C7BTMHEI.js.map → tp.ui-NF5ZYOHW.js.map} +0 -0
  905. /package/dist/{tvs.dt-PLRMK7OT.js.map → tvs.dt-43A4SSLG.js.map} +0 -0
  906. /package/dist/{tvs.dtcnv.categorical-IZUY2AQO.js.map → tvs.dtcnv.categorical-DYXHUNP2.js.map} +0 -0
  907. /package/dist/{tvs.dtcnv.continuous-ENV3RHHA.js.map → tvs.dtcnv.continuous-NOKNP4UG.js.map} +0 -0
  908. /package/dist/{tvs.dtfusion-2DVCV6AM.js.map → tvs.dtfusion-4NAOCC2X.js.map} +0 -0
  909. /package/dist/{tvs.dtitd-XNDIRQYU.js.map → tvs.dtitd-SZC6EITI.js.map} +0 -0
  910. /package/dist/{tvs.dtsnvindel-4D3G7XSF.js.map → tvs.dtsnvindel-EYSBCNQK.js.map} +0 -0
  911. /package/dist/{tvs.dtsv-QYMIMC4Z.js.map → tvs.dtsv-VSPWIIFO.js.map} +0 -0
  912. /package/dist/{tvs.samplelst-2KEU2ZWB.js.map → tvs.samplelst-3YQ4GKNG.js.map} +0 -0
  913. /package/dist/{tvs.termCollection-FEY746V5.js.map → tvs.termCollection-EVM4ATPW.js.map} +0 -0
  914. /package/dist/{vocabulary-BR4NJDPS.js.map → vocabulary-HCPEIO2P.js.map} +0 -0
  915. /package/dist/{wsi.direct-JWDUNHIO.js.map → wsi.direct-K2J6GGWY.js.map} +0 -0
@@ -1,1566 +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-NQNVLZOA.js";
25
- import {
26
- schemeCategory20
27
- } from "./chunk-V2OJLJSK.js";
28
- import {
29
- findgenemodel_bysymbol,
30
- gene_searchbox
31
- } from "./chunk-MNXL2UV5.js";
32
- import "./chunk-4XYQG3XU.js";
33
- import {
34
- appear2 as appear,
35
- disappear2 as disappear,
36
- font,
37
- newpane,
38
- sayerror
39
- } from "./chunk-55FABQU2.js";
40
- import "./chunk-HJ6L54YS.js";
41
- import "./chunk-KV4W2ACA.js";
42
- import "./chunk-UXD6G6G4.js";
43
- import {
44
- Menu
45
- } from "./chunk-ELJX3QIQ.js";
46
- import "./chunk-3FEP6B5T.js";
47
- import "./chunk-EEB5VE2A.js";
48
- import "./chunk-6RRZRISL.js";
49
- import "./chunk-2KM4PRQM.js";
50
- import {
51
- dofetch,
52
- dofetch2
53
- } from "./chunk-VA57CUC7.js";
54
- import "./chunk-BK6UDL7F.js";
55
- import "./chunk-KIAMLQ7S.js";
56
- import "./chunk-SB36AUG7.js";
57
- import "./chunk-WINIL2KN.js";
58
- import "./chunk-PF4DSFDR.js";
59
- import "./chunk-7X6NF7NI.js";
60
- import "./chunk-W5J3LTYS.js";
61
- import {
62
- area_default,
63
- axisBottom,
64
- axisLeft,
65
- axisTop,
66
- line_default,
67
- monotoneX,
68
- plasma
69
- } from "./chunk-Z2ZITHT4.js";
70
- import {
71
- band,
72
- linear,
73
- ordinal,
74
- sequential
75
- } from "./chunk-4OLM3KSB.js";
76
- import "./chunk-FXQXCOII.js";
77
- import "./chunk-TLT4YIG3.js";
78
- import "./chunk-5R63Q5KH.js";
79
- import {
80
- pointer_default
81
- } from "./chunk-I6Y4O3RR.js";
82
- import "./chunk-Q5RDQNIT.js";
83
- import "./chunk-DQC5FFGV.js";
84
- import "./chunk-HS5PO5ZQ.js";
85
-
86
- // ../node_modules/three/examples/jsm/loaders/PCDLoader.js
87
- var PCDLoader = class extends Loader {
88
- constructor(manager) {
89
- super(manager);
90
- this.littleEndian = true;
91
- }
92
- load(url, onLoad, onProgress, onError) {
93
- const scope = this;
94
- const loader = new FileLoader(scope.manager);
95
- loader.setPath(scope.path);
96
- loader.setResponseType("arraybuffer");
97
- loader.setRequestHeader(scope.requestHeader);
98
- loader.setWithCredentials(scope.withCredentials);
99
- loader.load(url, function(data) {
100
- try {
101
- onLoad(scope.parse(data));
102
- } catch (e) {
103
- if (onError) {
104
- onError(e);
105
- } else {
106
- console.error(e);
107
- }
108
- scope.manager.itemError(url);
109
- }
110
- }, onProgress, onError);
111
- }
112
- parse(data) {
113
- function decompressLZF(inData, outLength) {
114
- const inLength = inData.length;
115
- const outData = new Uint8Array(outLength);
116
- let inPtr = 0;
117
- let outPtr = 0;
118
- let ctrl;
119
- let len;
120
- let ref;
121
- do {
122
- ctrl = inData[inPtr++];
123
- if (ctrl < 1 << 5) {
124
- ctrl++;
125
- if (outPtr + ctrl > outLength) throw new Error("Output buffer is not large enough");
126
- if (inPtr + ctrl > inLength) throw new Error("Invalid compressed data");
127
- do {
128
- outData[outPtr++] = inData[inPtr++];
129
- } while (--ctrl);
130
- } else {
131
- len = ctrl >> 5;
132
- ref = outPtr - ((ctrl & 31) << 8) - 1;
133
- if (inPtr >= inLength) throw new Error("Invalid compressed data");
134
- if (len === 7) {
135
- len += inData[inPtr++];
136
- if (inPtr >= inLength) throw new Error("Invalid compressed data");
137
- }
138
- ref -= inData[inPtr++];
139
- if (outPtr + len + 2 > outLength) throw new Error("Output buffer is not large enough");
140
- if (ref < 0) throw new Error("Invalid compressed data");
141
- if (ref >= outPtr) throw new Error("Invalid compressed data");
142
- do {
143
- outData[outPtr++] = outData[ref++];
144
- } while (--len + 2);
145
- }
146
- } while (inPtr < inLength);
147
- return outData;
148
- }
149
- function parseHeader(data2) {
150
- const PCDheader2 = {};
151
- const result1 = data2.search(/[\r\n]DATA\s(\S*)\s/i);
152
- const result2 = /[\r\n]DATA\s(\S*)\s/i.exec(data2.slice(result1 - 1));
153
- PCDheader2.data = result2[1];
154
- PCDheader2.headerLen = result2[0].length + result1;
155
- PCDheader2.str = data2.slice(0, PCDheader2.headerLen);
156
- PCDheader2.str = PCDheader2.str.replace(/#.*/gi, "");
157
- PCDheader2.version = /VERSION (.*)/i.exec(PCDheader2.str);
158
- PCDheader2.fields = /FIELDS (.*)/i.exec(PCDheader2.str);
159
- PCDheader2.size = /SIZE (.*)/i.exec(PCDheader2.str);
160
- PCDheader2.type = /TYPE (.*)/i.exec(PCDheader2.str);
161
- PCDheader2.count = /COUNT (.*)/i.exec(PCDheader2.str);
162
- PCDheader2.width = /WIDTH (.*)/i.exec(PCDheader2.str);
163
- PCDheader2.height = /HEIGHT (.*)/i.exec(PCDheader2.str);
164
- PCDheader2.viewpoint = /VIEWPOINT (.*)/i.exec(PCDheader2.str);
165
- PCDheader2.points = /POINTS (.*)/i.exec(PCDheader2.str);
166
- if (PCDheader2.version !== null)
167
- PCDheader2.version = parseFloat(PCDheader2.version[1]);
168
- PCDheader2.fields = PCDheader2.fields !== null ? PCDheader2.fields[1].split(" ") : [];
169
- if (PCDheader2.type !== null)
170
- PCDheader2.type = PCDheader2.type[1].split(" ");
171
- if (PCDheader2.width !== null)
172
- PCDheader2.width = parseInt(PCDheader2.width[1]);
173
- if (PCDheader2.height !== null)
174
- PCDheader2.height = parseInt(PCDheader2.height[1]);
175
- if (PCDheader2.viewpoint !== null)
176
- PCDheader2.viewpoint = PCDheader2.viewpoint[1];
177
- if (PCDheader2.points !== null)
178
- PCDheader2.points = parseInt(PCDheader2.points[1], 10);
179
- if (PCDheader2.points === null)
180
- PCDheader2.points = PCDheader2.width * PCDheader2.height;
181
- if (PCDheader2.size !== null) {
182
- PCDheader2.size = PCDheader2.size[1].split(" ").map(function(x) {
183
- return parseInt(x, 10);
184
- });
185
- }
186
- if (PCDheader2.count !== null) {
187
- PCDheader2.count = PCDheader2.count[1].split(" ").map(function(x) {
188
- return parseInt(x, 10);
189
- });
190
- } else {
191
- PCDheader2.count = [];
192
- for (let i = 0, l = PCDheader2.fields.length; i < l; i++) {
193
- PCDheader2.count.push(1);
194
- }
195
- }
196
- PCDheader2.offset = {};
197
- let sizeSum = 0;
198
- for (let i = 0, l = PCDheader2.fields.length; i < l; i++) {
199
- if (PCDheader2.data === "ascii") {
200
- PCDheader2.offset[PCDheader2.fields[i]] = i;
201
- } else {
202
- PCDheader2.offset[PCDheader2.fields[i]] = sizeSum;
203
- sizeSum += PCDheader2.size[i] * PCDheader2.count[i];
204
- }
205
- }
206
- PCDheader2.rowSize = sizeSum;
207
- return PCDheader2;
208
- }
209
- const textData = new TextDecoder().decode(data);
210
- const PCDheader = parseHeader(textData);
211
- const position = [];
212
- const normal = [];
213
- const color = [];
214
- const intensity = [];
215
- const label = [];
216
- if (PCDheader.data === "ascii") {
217
- const offset = PCDheader.offset;
218
- const pcdData = textData.slice(PCDheader.headerLen);
219
- const lines = pcdData.split("\n");
220
- for (let i = 0, l = lines.length; i < l; i++) {
221
- if (lines[i] === "") continue;
222
- const line = lines[i].split(" ");
223
- if (offset.x !== void 0) {
224
- position.push(parseFloat(line[offset.x]));
225
- position.push(parseFloat(line[offset.y]));
226
- position.push(parseFloat(line[offset.z]));
227
- }
228
- if (offset.rgb !== void 0) {
229
- const rgb_field_index = PCDheader.fields.findIndex((field) => field === "rgb");
230
- const rgb_type = PCDheader.type[rgb_field_index];
231
- const float = parseFloat(line[offset.rgb]);
232
- let rgb = float;
233
- if (rgb_type === "F") {
234
- const farr = new Float32Array(1);
235
- farr[0] = float;
236
- rgb = new Int32Array(farr.buffer)[0];
237
- }
238
- const r = rgb >> 16 & 255;
239
- const g = rgb >> 8 & 255;
240
- const b = rgb >> 0 & 255;
241
- color.push(r / 255, g / 255, b / 255);
242
- }
243
- if (offset.normal_x !== void 0) {
244
- normal.push(parseFloat(line[offset.normal_x]));
245
- normal.push(parseFloat(line[offset.normal_y]));
246
- normal.push(parseFloat(line[offset.normal_z]));
247
- }
248
- if (offset.intensity !== void 0) {
249
- intensity.push(parseFloat(line[offset.intensity]));
250
- }
251
- if (offset.label !== void 0) {
252
- label.push(parseInt(line[offset.label]));
253
- }
254
- }
255
- }
256
- if (PCDheader.data === "binary_compressed") {
257
- const sizes = new Uint32Array(data.slice(PCDheader.headerLen, PCDheader.headerLen + 8));
258
- const compressedSize = sizes[0];
259
- const decompressedSize = sizes[1];
260
- const decompressed = decompressLZF(new Uint8Array(data, PCDheader.headerLen + 8, compressedSize), decompressedSize);
261
- const dataview = new DataView(decompressed.buffer);
262
- const offset = PCDheader.offset;
263
- for (let i = 0; i < PCDheader.points; i++) {
264
- if (offset.x !== void 0) {
265
- const xIndex = PCDheader.fields.indexOf("x");
266
- const yIndex = PCDheader.fields.indexOf("y");
267
- const zIndex = PCDheader.fields.indexOf("z");
268
- position.push(dataview.getFloat32(PCDheader.points * offset.x + PCDheader.size[xIndex] * i, this.littleEndian));
269
- position.push(dataview.getFloat32(PCDheader.points * offset.y + PCDheader.size[yIndex] * i, this.littleEndian));
270
- position.push(dataview.getFloat32(PCDheader.points * offset.z + PCDheader.size[zIndex] * i, this.littleEndian));
271
- }
272
- if (offset.rgb !== void 0) {
273
- const rgbIndex = PCDheader.fields.indexOf("rgb");
274
- color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[rgbIndex] * i + 2) / 255);
275
- color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[rgbIndex] * i + 1) / 255);
276
- color.push(dataview.getUint8(PCDheader.points * offset.rgb + PCDheader.size[rgbIndex] * i + 0) / 255);
277
- }
278
- if (offset.normal_x !== void 0) {
279
- const xIndex = PCDheader.fields.indexOf("normal_x");
280
- const yIndex = PCDheader.fields.indexOf("normal_y");
281
- const zIndex = PCDheader.fields.indexOf("normal_z");
282
- normal.push(dataview.getFloat32(PCDheader.points * offset.normal_x + PCDheader.size[xIndex] * i, this.littleEndian));
283
- normal.push(dataview.getFloat32(PCDheader.points * offset.normal_y + PCDheader.size[yIndex] * i, this.littleEndian));
284
- normal.push(dataview.getFloat32(PCDheader.points * offset.normal_z + PCDheader.size[zIndex] * i, this.littleEndian));
285
- }
286
- if (offset.intensity !== void 0) {
287
- const intensityIndex = PCDheader.fields.indexOf("intensity");
288
- intensity.push(dataview.getFloat32(PCDheader.points * offset.intensity + PCDheader.size[intensityIndex] * i, this.littleEndian));
289
- }
290
- if (offset.label !== void 0) {
291
- const labelIndex = PCDheader.fields.indexOf("label");
292
- label.push(dataview.getInt32(PCDheader.points * offset.label + PCDheader.size[labelIndex] * i, this.littleEndian));
293
- }
294
- }
295
- }
296
- if (PCDheader.data === "binary") {
297
- const dataview = new DataView(data, PCDheader.headerLen);
298
- const offset = PCDheader.offset;
299
- for (let i = 0, row = 0; i < PCDheader.points; i++, row += PCDheader.rowSize) {
300
- if (offset.x !== void 0) {
301
- position.push(dataview.getFloat32(row + offset.x, this.littleEndian));
302
- position.push(dataview.getFloat32(row + offset.y, this.littleEndian));
303
- position.push(dataview.getFloat32(row + offset.z, this.littleEndian));
304
- }
305
- if (offset.rgb !== void 0) {
306
- color.push(dataview.getUint8(row + offset.rgb + 2) / 255);
307
- color.push(dataview.getUint8(row + offset.rgb + 1) / 255);
308
- color.push(dataview.getUint8(row + offset.rgb + 0) / 255);
309
- }
310
- if (offset.normal_x !== void 0) {
311
- normal.push(dataview.getFloat32(row + offset.normal_x, this.littleEndian));
312
- normal.push(dataview.getFloat32(row + offset.normal_y, this.littleEndian));
313
- normal.push(dataview.getFloat32(row + offset.normal_z, this.littleEndian));
314
- }
315
- if (offset.intensity !== void 0) {
316
- intensity.push(dataview.getFloat32(row + offset.intensity, this.littleEndian));
317
- }
318
- if (offset.label !== void 0) {
319
- label.push(dataview.getInt32(row + offset.label, this.littleEndian));
320
- }
321
- }
322
- }
323
- const geometry = new BufferGeometry();
324
- if (position.length > 0) geometry.setAttribute("position", new Float32BufferAttribute(position, 3));
325
- if (normal.length > 0) geometry.setAttribute("normal", new Float32BufferAttribute(normal, 3));
326
- if (color.length > 0) geometry.setAttribute("color", new Float32BufferAttribute(color, 3));
327
- if (intensity.length > 0) geometry.setAttribute("intensity", new Float32BufferAttribute(intensity, 1));
328
- if (label.length > 0) geometry.setAttribute("label", new Int32BufferAttribute(label, 1));
329
- geometry.computeBoundingSphere();
330
- const material = new PointsMaterial({ size: 5e-3 });
331
- if (color.length > 0) {
332
- material.vertexColors = true;
333
- }
334
- return new Points(geometry, material);
335
- }
336
- };
337
-
338
- // ../public/static/js/WebGL.js
339
- function isWebGLAvailable() {
340
- try {
341
- var canvas = document.createElement("canvas");
342
- return !!(window.WebGLRenderingContext && (canvas.getContext("webgl") || canvas.getContext("experimental-webgl")));
343
- } catch (e) {
344
- return false;
345
- }
346
- }
347
- function getWebGLErrorMessage() {
348
- return this.getErrorMessage(1);
349
- }
350
-
351
- // ../node_modules/three/examples/jsm/controls/TrackballControls.js
352
- var _changeEvent = { type: "change" };
353
- var _startEvent = { type: "start" };
354
- var _endEvent = { type: "end" };
355
- var TrackballControls = class extends EventDispatcher {
356
- constructor(object, domElement) {
357
- super();
358
- const scope = this;
359
- const STATE = { NONE: -1, ROTATE: 0, ZOOM: 1, PAN: 2, TOUCH_ROTATE: 3, TOUCH_ZOOM_PAN: 4 };
360
- this.object = object;
361
- this.domElement = domElement;
362
- this.domElement.style.touchAction = "none";
363
- this.enabled = true;
364
- this.screen = { left: 0, top: 0, width: 0, height: 0 };
365
- this.rotateSpeed = 1;
366
- this.zoomSpeed = 1.2;
367
- this.panSpeed = 0.3;
368
- this.noRotate = false;
369
- this.noZoom = false;
370
- this.noPan = false;
371
- this.staticMoving = false;
372
- this.dynamicDampingFactor = 0.2;
373
- this.minDistance = 0;
374
- this.maxDistance = Infinity;
375
- this.minZoom = 0;
376
- this.maxZoom = Infinity;
377
- this.keys = [
378
- "KeyA",
379
- "KeyS",
380
- "KeyD"
381
- /*D*/
382
- ];
383
- this.mouseButtons = { LEFT: MOUSE.ROTATE, MIDDLE: MOUSE.DOLLY, RIGHT: MOUSE.PAN };
384
- this.target = new Vector3();
385
- const EPS = 1e-6;
386
- const lastPosition = new Vector3();
387
- let lastZoom = 1;
388
- let _state = STATE.NONE, _keyState = STATE.NONE, _touchZoomDistanceStart = 0, _touchZoomDistanceEnd = 0, _lastAngle = 0;
389
- 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 = {};
390
- this.target0 = this.target.clone();
391
- this.position0 = this.object.position.clone();
392
- this.up0 = this.object.up.clone();
393
- this.zoom0 = this.object.zoom;
394
- this.handleResize = function() {
395
- const box = scope.domElement.getBoundingClientRect();
396
- const d = scope.domElement.ownerDocument.documentElement;
397
- scope.screen.left = box.left + window.pageXOffset - d.clientLeft;
398
- scope.screen.top = box.top + window.pageYOffset - d.clientTop;
399
- scope.screen.width = box.width;
400
- scope.screen.height = box.height;
401
- };
402
- const getMouseOnScreen = (function() {
403
- const vector = new Vector2();
404
- return function getMouseOnScreen2(pageX, pageY) {
405
- vector.set(
406
- (pageX - scope.screen.left) / scope.screen.width,
407
- (pageY - scope.screen.top) / scope.screen.height
408
- );
409
- return vector;
410
- };
411
- })();
412
- const getMouseOnCircle = (function() {
413
- const vector = new Vector2();
414
- return function getMouseOnCircle2(pageX, pageY) {
415
- vector.set(
416
- (pageX - scope.screen.width * 0.5 - scope.screen.left) / (scope.screen.width * 0.5),
417
- (scope.screen.height + 2 * (scope.screen.top - pageY)) / scope.screen.width
418
- // screen.width intentional
419
- );
420
- return vector;
421
- };
422
- })();
423
- this.rotateCamera = (function() {
424
- const axis = new Vector3(), quaternion = new Quaternion(), eyeDirection = new Vector3(), objectUpDirection = new Vector3(), objectSidewaysDirection = new Vector3(), moveDirection = new Vector3();
425
- return function rotateCamera() {
426
- moveDirection.set(_moveCurr.x - _movePrev.x, _moveCurr.y - _movePrev.y, 0);
427
- let angle = moveDirection.length();
428
- if (angle) {
429
- _eye.copy(scope.object.position).sub(scope.target);
430
- eyeDirection.copy(_eye).normalize();
431
- objectUpDirection.copy(scope.object.up).normalize();
432
- objectSidewaysDirection.crossVectors(objectUpDirection, eyeDirection).normalize();
433
- objectUpDirection.setLength(_moveCurr.y - _movePrev.y);
434
- objectSidewaysDirection.setLength(_moveCurr.x - _movePrev.x);
435
- moveDirection.copy(objectUpDirection.add(objectSidewaysDirection));
436
- axis.crossVectors(moveDirection, _eye).normalize();
437
- angle *= scope.rotateSpeed;
438
- quaternion.setFromAxisAngle(axis, angle);
439
- _eye.applyQuaternion(quaternion);
440
- scope.object.up.applyQuaternion(quaternion);
441
- _lastAxis.copy(axis);
442
- _lastAngle = angle;
443
- } else if (!scope.staticMoving && _lastAngle) {
444
- _lastAngle *= Math.sqrt(1 - scope.dynamicDampingFactor);
445
- _eye.copy(scope.object.position).sub(scope.target);
446
- quaternion.setFromAxisAngle(_lastAxis, _lastAngle);
447
- _eye.applyQuaternion(quaternion);
448
- scope.object.up.applyQuaternion(quaternion);
449
- }
450
- _movePrev.copy(_moveCurr);
451
- };
452
- })();
453
- this.zoomCamera = function() {
454
- let factor;
455
- if (_state === STATE.TOUCH_ZOOM_PAN) {
456
- factor = _touchZoomDistanceStart / _touchZoomDistanceEnd;
457
- _touchZoomDistanceStart = _touchZoomDistanceEnd;
458
- if (scope.object.isPerspectiveCamera) {
459
- _eye.multiplyScalar(factor);
460
- } else if (scope.object.isOrthographicCamera) {
461
- scope.object.zoom = MathUtils.clamp(scope.object.zoom / factor, scope.minZoom, scope.maxZoom);
462
- if (lastZoom !== scope.object.zoom) {
463
- scope.object.updateProjectionMatrix();
464
- }
465
- } else {
466
- console.warn("THREE.TrackballControls: Unsupported camera type");
467
- }
468
- } else {
469
- factor = 1 + (_zoomEnd.y - _zoomStart.y) * scope.zoomSpeed;
470
- if (factor !== 1 && factor > 0) {
471
- if (scope.object.isPerspectiveCamera) {
472
- _eye.multiplyScalar(factor);
473
- } else if (scope.object.isOrthographicCamera) {
474
- scope.object.zoom = MathUtils.clamp(scope.object.zoom / factor, scope.minZoom, scope.maxZoom);
475
- if (lastZoom !== scope.object.zoom) {
476
- scope.object.updateProjectionMatrix();
477
- }
478
- } else {
479
- console.warn("THREE.TrackballControls: Unsupported camera type");
480
- }
481
- }
482
- if (scope.staticMoving) {
483
- _zoomStart.copy(_zoomEnd);
484
- } else {
485
- _zoomStart.y += (_zoomEnd.y - _zoomStart.y) * this.dynamicDampingFactor;
486
- }
487
- }
488
- };
489
- this.panCamera = (function() {
490
- const mouseChange = new Vector2(), objectUp = new Vector3(), pan = new Vector3();
491
- return function panCamera() {
492
- mouseChange.copy(_panEnd).sub(_panStart);
493
- if (mouseChange.lengthSq()) {
494
- if (scope.object.isOrthographicCamera) {
495
- const scale_x = (scope.object.right - scope.object.left) / scope.object.zoom / scope.domElement.clientWidth;
496
- const scale_y = (scope.object.top - scope.object.bottom) / scope.object.zoom / scope.domElement.clientWidth;
497
- mouseChange.x *= scale_x;
498
- mouseChange.y *= scale_y;
499
- }
500
- mouseChange.multiplyScalar(_eye.length() * scope.panSpeed);
501
- pan.copy(_eye).cross(scope.object.up).setLength(mouseChange.x);
502
- pan.add(objectUp.copy(scope.object.up).setLength(mouseChange.y));
503
- scope.object.position.add(pan);
504
- scope.target.add(pan);
505
- if (scope.staticMoving) {
506
- _panStart.copy(_panEnd);
507
- } else {
508
- _panStart.add(mouseChange.subVectors(_panEnd, _panStart).multiplyScalar(scope.dynamicDampingFactor));
509
- }
510
- }
511
- };
512
- })();
513
- this.checkDistances = function() {
514
- if (!scope.noZoom || !scope.noPan) {
515
- if (_eye.lengthSq() > scope.maxDistance * scope.maxDistance) {
516
- scope.object.position.addVectors(scope.target, _eye.setLength(scope.maxDistance));
517
- _zoomStart.copy(_zoomEnd);
518
- }
519
- if (_eye.lengthSq() < scope.minDistance * scope.minDistance) {
520
- scope.object.position.addVectors(scope.target, _eye.setLength(scope.minDistance));
521
- _zoomStart.copy(_zoomEnd);
522
- }
523
- }
524
- };
525
- this.update = function() {
526
- _eye.subVectors(scope.object.position, scope.target);
527
- if (!scope.noRotate) {
528
- scope.rotateCamera();
529
- }
530
- if (!scope.noZoom) {
531
- scope.zoomCamera();
532
- }
533
- if (!scope.noPan) {
534
- scope.panCamera();
535
- }
536
- scope.object.position.addVectors(scope.target, _eye);
537
- if (scope.object.isPerspectiveCamera) {
538
- scope.checkDistances();
539
- scope.object.lookAt(scope.target);
540
- if (lastPosition.distanceToSquared(scope.object.position) > EPS) {
541
- scope.dispatchEvent(_changeEvent);
542
- lastPosition.copy(scope.object.position);
543
- }
544
- } else if (scope.object.isOrthographicCamera) {
545
- scope.object.lookAt(scope.target);
546
- if (lastPosition.distanceToSquared(scope.object.position) > EPS || lastZoom !== scope.object.zoom) {
547
- scope.dispatchEvent(_changeEvent);
548
- lastPosition.copy(scope.object.position);
549
- lastZoom = scope.object.zoom;
550
- }
551
- } else {
552
- console.warn("THREE.TrackballControls: Unsupported camera type");
553
- }
554
- };
555
- this.reset = function() {
556
- _state = STATE.NONE;
557
- _keyState = STATE.NONE;
558
- scope.target.copy(scope.target0);
559
- scope.object.position.copy(scope.position0);
560
- scope.object.up.copy(scope.up0);
561
- scope.object.zoom = scope.zoom0;
562
- scope.object.updateProjectionMatrix();
563
- _eye.subVectors(scope.object.position, scope.target);
564
- scope.object.lookAt(scope.target);
565
- scope.dispatchEvent(_changeEvent);
566
- lastPosition.copy(scope.object.position);
567
- lastZoom = scope.object.zoom;
568
- };
569
- function onPointerDown(event) {
570
- if (scope.enabled === false) return;
571
- if (_pointers.length === 0) {
572
- scope.domElement.setPointerCapture(event.pointerId);
573
- scope.domElement.addEventListener("pointermove", onPointerMove);
574
- scope.domElement.addEventListener("pointerup", onPointerUp);
575
- }
576
- addPointer(event);
577
- if (event.pointerType === "touch") {
578
- onTouchStart(event);
579
- } else {
580
- onMouseDown(event);
581
- }
582
- }
583
- function onPointerMove(event) {
584
- if (scope.enabled === false) return;
585
- if (event.pointerType === "touch") {
586
- onTouchMove(event);
587
- } else {
588
- onMouseMove(event);
589
- }
590
- }
591
- function onPointerUp(event) {
592
- if (scope.enabled === false) return;
593
- if (event.pointerType === "touch") {
594
- onTouchEnd(event);
595
- } else {
596
- onMouseUp();
597
- }
598
- removePointer(event);
599
- if (_pointers.length === 0) {
600
- scope.domElement.releasePointerCapture(event.pointerId);
601
- scope.domElement.removeEventListener("pointermove", onPointerMove);
602
- scope.domElement.removeEventListener("pointerup", onPointerUp);
603
- }
604
- }
605
- function onPointerCancel(event) {
606
- removePointer(event);
607
- }
608
- function keydown(event) {
609
- if (scope.enabled === false) return;
610
- window.removeEventListener("keydown", keydown);
611
- if (_keyState !== STATE.NONE) {
612
- return;
613
- } else if (event.code === scope.keys[STATE.ROTATE] && !scope.noRotate) {
614
- _keyState = STATE.ROTATE;
615
- } else if (event.code === scope.keys[STATE.ZOOM] && !scope.noZoom) {
616
- _keyState = STATE.ZOOM;
617
- } else if (event.code === scope.keys[STATE.PAN] && !scope.noPan) {
618
- _keyState = STATE.PAN;
619
- }
620
- }
621
- function keyup() {
622
- if (scope.enabled === false) return;
623
- _keyState = STATE.NONE;
624
- window.addEventListener("keydown", keydown);
625
- }
626
- function onMouseDown(event) {
627
- if (_state === STATE.NONE) {
628
- switch (event.button) {
629
- case scope.mouseButtons.LEFT:
630
- _state = STATE.ROTATE;
631
- break;
632
- case scope.mouseButtons.MIDDLE:
633
- _state = STATE.ZOOM;
634
- break;
635
- case scope.mouseButtons.RIGHT:
636
- _state = STATE.PAN;
637
- break;
638
- }
639
- }
640
- const state = _keyState !== STATE.NONE ? _keyState : _state;
641
- if (state === STATE.ROTATE && !scope.noRotate) {
642
- _moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
643
- _movePrev.copy(_moveCurr);
644
- } else if (state === STATE.ZOOM && !scope.noZoom) {
645
- _zoomStart.copy(getMouseOnScreen(event.pageX, event.pageY));
646
- _zoomEnd.copy(_zoomStart);
647
- } else if (state === STATE.PAN && !scope.noPan) {
648
- _panStart.copy(getMouseOnScreen(event.pageX, event.pageY));
649
- _panEnd.copy(_panStart);
650
- }
651
- scope.dispatchEvent(_startEvent);
652
- }
653
- function onMouseMove(event) {
654
- const state = _keyState !== STATE.NONE ? _keyState : _state;
655
- if (state === STATE.ROTATE && !scope.noRotate) {
656
- _movePrev.copy(_moveCurr);
657
- _moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
658
- } else if (state === STATE.ZOOM && !scope.noZoom) {
659
- _zoomEnd.copy(getMouseOnScreen(event.pageX, event.pageY));
660
- } else if (state === STATE.PAN && !scope.noPan) {
661
- _panEnd.copy(getMouseOnScreen(event.pageX, event.pageY));
662
- }
663
- }
664
- function onMouseUp() {
665
- _state = STATE.NONE;
666
- scope.dispatchEvent(_endEvent);
667
- }
668
- function onMouseWheel(event) {
669
- if (scope.enabled === false) return;
670
- if (scope.noZoom === true) return;
671
- event.preventDefault();
672
- switch (event.deltaMode) {
673
- case 2:
674
- _zoomStart.y -= event.deltaY * 0.025;
675
- break;
676
- case 1:
677
- _zoomStart.y -= event.deltaY * 0.01;
678
- break;
679
- default:
680
- _zoomStart.y -= event.deltaY * 25e-5;
681
- break;
682
- }
683
- scope.dispatchEvent(_startEvent);
684
- scope.dispatchEvent(_endEvent);
685
- }
686
- function onTouchStart(event) {
687
- trackPointer(event);
688
- switch (_pointers.length) {
689
- case 1:
690
- _state = STATE.TOUCH_ROTATE;
691
- _moveCurr.copy(getMouseOnCircle(_pointers[0].pageX, _pointers[0].pageY));
692
- _movePrev.copy(_moveCurr);
693
- break;
694
- default:
695
- _state = STATE.TOUCH_ZOOM_PAN;
696
- const dx = _pointers[0].pageX - _pointers[1].pageX;
697
- const dy = _pointers[0].pageY - _pointers[1].pageY;
698
- _touchZoomDistanceEnd = _touchZoomDistanceStart = Math.sqrt(dx * dx + dy * dy);
699
- const x = (_pointers[0].pageX + _pointers[1].pageX) / 2;
700
- const y = (_pointers[0].pageY + _pointers[1].pageY) / 2;
701
- _panStart.copy(getMouseOnScreen(x, y));
702
- _panEnd.copy(_panStart);
703
- break;
704
- }
705
- scope.dispatchEvent(_startEvent);
706
- }
707
- function onTouchMove(event) {
708
- trackPointer(event);
709
- switch (_pointers.length) {
710
- case 1:
711
- _movePrev.copy(_moveCurr);
712
- _moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
713
- break;
714
- default:
715
- const position = getSecondPointerPosition(event);
716
- const dx = event.pageX - position.x;
717
- const dy = event.pageY - position.y;
718
- _touchZoomDistanceEnd = Math.sqrt(dx * dx + dy * dy);
719
- const x = (event.pageX + position.x) / 2;
720
- const y = (event.pageY + position.y) / 2;
721
- _panEnd.copy(getMouseOnScreen(x, y));
722
- break;
723
- }
724
- }
725
- function onTouchEnd(event) {
726
- switch (_pointers.length) {
727
- case 0:
728
- _state = STATE.NONE;
729
- break;
730
- case 1:
731
- _state = STATE.TOUCH_ROTATE;
732
- _moveCurr.copy(getMouseOnCircle(event.pageX, event.pageY));
733
- _movePrev.copy(_moveCurr);
734
- break;
735
- case 2:
736
- _state = STATE.TOUCH_ZOOM_PAN;
737
- for (let i = 0; i < _pointers.length; i++) {
738
- if (_pointers[i].pointerId !== event.pointerId) {
739
- const position = _pointerPositions[_pointers[i].pointerId];
740
- _moveCurr.copy(getMouseOnCircle(position.x, position.y));
741
- _movePrev.copy(_moveCurr);
742
- break;
743
- }
744
- }
745
- break;
746
- }
747
- scope.dispatchEvent(_endEvent);
748
- }
749
- function contextmenu(event) {
750
- if (scope.enabled === false) return;
751
- event.preventDefault();
752
- }
753
- function addPointer(event) {
754
- _pointers.push(event);
755
- }
756
- function removePointer(event) {
757
- delete _pointerPositions[event.pointerId];
758
- for (let i = 0; i < _pointers.length; i++) {
759
- if (_pointers[i].pointerId == event.pointerId) {
760
- _pointers.splice(i, 1);
761
- return;
762
- }
763
- }
764
- }
765
- function trackPointer(event) {
766
- let position = _pointerPositions[event.pointerId];
767
- if (position === void 0) {
768
- position = new Vector2();
769
- _pointerPositions[event.pointerId] = position;
770
- }
771
- position.set(event.pageX, event.pageY);
772
- }
773
- function getSecondPointerPosition(event) {
774
- const pointer = event.pointerId === _pointers[0].pointerId ? _pointers[1] : _pointers[0];
775
- return _pointerPositions[pointer.pointerId];
776
- }
777
- this.dispose = function() {
778
- scope.domElement.removeEventListener("contextmenu", contextmenu);
779
- scope.domElement.removeEventListener("pointerdown", onPointerDown);
780
- scope.domElement.removeEventListener("pointercancel", onPointerCancel);
781
- scope.domElement.removeEventListener("wheel", onMouseWheel);
782
- scope.domElement.removeEventListener("pointermove", onPointerMove);
783
- scope.domElement.removeEventListener("pointerup", onPointerUp);
784
- window.removeEventListener("keydown", keydown);
785
- window.removeEventListener("keyup", keyup);
786
- };
787
- this.domElement.addEventListener("contextmenu", contextmenu);
788
- this.domElement.addEventListener("pointerdown", onPointerDown);
789
- this.domElement.addEventListener("pointercancel", onPointerCancel);
790
- this.domElement.addEventListener("wheel", onMouseWheel, { passive: false });
791
- window.addEventListener("keydown", keydown);
792
- window.addEventListener("keyup", keyup);
793
- this.handleResize();
794
- this.update();
795
- }
796
- };
797
-
798
- // src/singlecell.js
799
- async function init(arg, holder) {
800
- try {
801
- const obj = await load_json(arg);
802
- validate_obj(obj);
803
- obj.genome = arg.genome;
804
- obj.holder = holder.style("position", "relative");
805
- await init_view(obj);
806
- init_controlpanel(obj);
807
- await pcd_pipeline(obj);
808
- make_legend(arg, obj);
809
- } catch (e) {
810
- sayerror(holder, e.message || e);
811
- }
812
- }
813
- async function load_json(arg) {
814
- if (!arg.jsonfile) throw ".jsonfile missing";
815
- const tmp = await dofetch("textfile", { file: arg.jsonfile });
816
- if (tmp.error) throw tmp.error;
817
- return JSON.parse(tmp.text);
818
- }
819
- function validate_obj(obj) {
820
- if (!obj.cells) throw ".cells{} missing";
821
- if (!obj.cells.file) throw ".cells.file missing";
822
- if (!obj.cells.axis2columnidx) throw ".cells.axis2columnidx missing";
823
- if (obj.cells.categories) {
824
- if (!Array.isArray(obj.cells.categories)) throw ".cells.categories should be an array";
825
- if (obj.cells.categories.length == 0) throw ".cells.categories[] is empty array";
826
- for (const c of obj.cells.categories) {
827
- if (!Number.isInteger(c.columnidx)) throw "columnidx missing from category " + c;
828
- if (c.autocolor) {
829
- c.autocolor = ordinal(schemeCategory20);
830
- }
831
- }
832
- if (!Number.isInteger(obj.use_category_index)) {
833
- obj.use_category_index = 0;
834
- }
835
- if (!obj.cells.categories[obj.use_category_index]) throw "use_category_index out of bound";
836
- if (!obj.cells.categories[obj.use_category_index].hidden_types)
837
- obj.cells.categories[obj.use_category_index].hidden_types = [];
838
- }
839
- if (obj.gene_expression) {
840
- if (!obj.gene_expression.file) throw ".gene_expression.file missing";
841
- if (!Number.isInteger(obj.cells.barcodecolumnidx))
842
- throw ".gene_expression in use but .cells.barcodecolumnidx is missing";
843
- }
844
- if (!obj.width) obj.width = window.innerWidth * 0.9;
845
- if (!obj.height) obj.height = window.innerHeight * 0.9;
846
- }
847
- async function pcd_pipeline(obj) {
848
- if (Number.isInteger(obj.use_category_index)) {
849
- if (!obj.cells.categories[obj.use_category_index].hidden_types)
850
- obj.cells.categories[obj.use_category_index].hidden_types = [];
851
- }
852
- const data = await load_cell_pcd(obj);
853
- obj.data_sphere_r = data.data_sphere_r;
854
- if (!obj.camera.position.z) {
855
- obj.camera.position.z = obj.data_sphere_r * 3;
856
- obj.controls.maxDistance = obj.data_sphere_r * 4;
857
- obj.controls.minDistance = obj.data_sphere_r / 10;
858
- }
859
- const enc = new TextEncoder();
860
- const pcd_buffer = enc.encode(data.pcddata).buffer;
861
- render_cloud(obj, pcd_buffer);
862
- render_controlpanel(obj, data);
863
- animate();
864
- function animate() {
865
- requestAnimationFrame(animate);
866
- obj.controls.update();
867
- obj.renderer.render(obj.scene, obj.camera);
868
- }
869
- }
870
- async function load_cell_pcd(obj) {
871
- 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...");
872
- const arg = {
873
- genome: obj.genome.name,
874
- textfile: obj.cells.file,
875
- delimiter: obj.cells.delimiter || " ",
876
- getpcd: {
877
- coord: obj.cells.axis2columnidx
878
- }
879
- };
880
- if (Number.isInteger(obj.use_category_index)) {
881
- if (!obj.cells.categories) throw "using category index but cells.categories[] missing";
882
- const cat = obj.cells.categories[obj.use_category_index];
883
- if (!cat) throw "category array index out of bound";
884
- arg.getpcd.category_index = cat.columnidx;
885
- if (cat.autocolor) {
886
- arg.getpcd.category_autocolor = true;
887
- if (cat.values_count) arg.getpcd.values_count = cat.values_count;
888
- } else if (cat.values) {
889
- arg.getpcd.category_customcolor = true;
890
- arg.getpcd.cat_values = cat.values;
891
- } else {
892
- if (!cat.autocolor && !cat.values) throw "categories.values[] are not defined";
893
- throw "unknow coloring scheme for category " + cat.name;
894
- }
895
- if (cat.hidden_types) {
896
- arg.hidden_types = cat.hidden_types;
897
- }
898
- if (obj.background_color) {
899
- arg.background_color = obj.background_color;
900
- }
901
- if (!cat.customorder) {
902
- arg.getpcd.category_autoorder = true;
903
- } else if (cat.customorder && cat.values) {
904
- arg.getpcd.category_customorder = true;
905
- arg.getpcd.cat_values = cat.values;
906
- } else {
907
- if (cat.customorder && !cat.values) throw "categories.values[] are not defined";
908
- throw "unknow ordering scheme for category " + cat.name;
909
- }
910
- obj.menu_button.html(cat.name + "&nbsp;&nbsp;&#9660;");
911
- } else if (Number.isInteger(obj.use_gene_index)) {
912
- const gene = obj.gene_expression.genes[obj.use_gene_index];
913
- obj.menu_button.html("Gene : " + gene.gene + "&nbsp;&nbsp;&#9660;");
914
- arg.getpcd.gene_expression = {
915
- file: obj.gene_expression.file,
916
- barcodecolumnidx: obj.cells.barcodecolumnidx,
917
- chr: gene.chr,
918
- start: gene.start,
919
- stop: gene.stop,
920
- autoscale: true,
921
- genename: gene.gene,
922
- color_min: obj.gene_expression.color_min,
923
- color_max: obj.gene_expression.color_max
924
- };
925
- if (obj.gene_expression.color_no_exp) arg.getpcd.gene_expression.color_no_exp = obj.gene_expression.color_no_exp;
926
- } else {
927
- throw "unknown method to color the cells";
928
- }
929
- return dofetch("singlecell", arg).then((data) => {
930
- if (data.error) throw data.error;
931
- wait.remove();
932
- return data;
933
- });
934
- }
935
- async function init_view(obj) {
936
- if (isWebGLAvailable() === false) {
937
- obj.holder.node().appendChild(getWebGLErrorMessage());
938
- return;
939
- }
940
- obj.scene = new Scene();
941
- if (obj.background_color) {
942
- obj.scene.background = new Color(obj.background_color);
943
- } else {
944
- obj.scene.background = new Color(16777215);
945
- }
946
- const default_zoom = obj.default_zoom ? 100 - obj.default_zoom : 45;
947
- obj.camera = new PerspectiveCamera(default_zoom, obj.width / obj.height, 0.1, 1e3);
948
- obj.camera.position.x = obj.canvas_2d ? 0 : 20;
949
- obj.camera.position.y = obj.canvas_2d ? 0 : -10;
950
- if (obj.canvas_2d) {
951
- obj.camera.up.set(0, 1, 0);
952
- } else {
953
- obj.camera.up.set(0, 0, 1);
954
- }
955
- obj.renderer = new WebGLRenderer({ antialias: true, preserveDrawingBuffer: true });
956
- obj.renderer.setPixelRatio(window.devicePixelRatio);
957
- obj.renderer.setSize(obj.width, obj.height);
958
- obj.renderer.domElement.style.backgroundColor = "#ffffff";
959
- obj.renderer.domElement.style.border = "solid #dddddd 2px";
960
- obj.renderer.outputColorSpace = LinearSRGBColorSpace;
961
- obj.renderer.toneMapping = NoToneMapping;
962
- obj.holder.style("display", "inline-block").style("position", "relative").node().appendChild(obj.renderer.domElement);
963
- obj.controls = new TrackballControls(obj.camera, obj.renderer.domElement);
964
- obj.controls.rotateSpeed = obj.canvas_2d ? 0 : 2;
965
- obj.controls.zoomSpeed = obj.canvas_2d ? 3 : 0.7;
966
- obj.controls.panSpeed = obj.canvas_2d ? 3 : 0.7;
967
- obj.controls.noZoom = true;
968
- obj.controls.noPan = false;
969
- obj.controls.staticMoving = true;
970
- obj.controls.dynamicDampingFactor = 0.3;
971
- obj.scene.add(obj.camera);
972
- obj.renderer.render(obj.scene, obj.camera);
973
- obj.controls.update();
974
- }
975
- function render_cloud(obj, pcd_buffer) {
976
- obj.scene.children.forEach(function(v, i) {
977
- if (v.material) {
978
- v.material.dispose();
979
- v.geometry.dispose();
980
- obj.scene.remove(v);
981
- }
982
- });
983
- const loader = new PCDLoader();
984
- const points = loader.parse(pcd_buffer, "");
985
- const newMat = new PointsMaterial({
986
- size: points.material.size,
987
- vertexColors: true,
988
- color: 16777215
989
- });
990
- points.material = newMat;
991
- points.material.vertexColors = true;
992
- points.material.color.set(16777215);
993
- points.material.needsUpdate = true;
994
- if (obj.point_size) {
995
- points.material.size = obj.point_size;
996
- } else {
997
- points.material.size = obj.canvas_2d ? 0.3 : 0.05;
998
- }
999
- obj.scene.add(points);
1000
- obj.center = points.geometry.boundingSphere.center;
1001
- obj.controls.target.set(obj.center.x, obj.center.y, obj.center.z);
1002
- obj.controls.update();
1003
- }
1004
- function init_controlpanel(obj) {
1005
- obj.menu = new Menu();
1006
- obj.menu.d.style("padding", "3px");
1007
- obj.settings = new Menu();
1008
- obj.settings.d.style("padding", "3px");
1009
- 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");
1010
- obj.menu_button = panel.append("button").style("display", "inline-block").style("padding", "4px").on("click", () => make_menu(obj));
1011
- 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", () => {
1012
- obj.minimize_btn.classed("active", obj.minimize_btn.classed("active") ? false : true);
1013
- if (obj.minimize_btn.classed("active")) {
1014
- obj.minimize_btn.text(" SHOW");
1015
- obj.menu_output.style("display", "none");
1016
- } else {
1017
- obj.minimize_btn.text(" HIDE");
1018
- obj.menu_output.style("display", "block");
1019
- }
1020
- }).on("mouseover", () => {
1021
- minimize_btn.style("text-decoration", "underline");
1022
- }).on("mouseout", () => {
1023
- minimize_btn.style("text-decoration", "none");
1024
- });
1025
- obj.use_background_color = 0;
1026
- 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", () => {
1027
- config_btn.style("text-decoration", "underline");
1028
- }).on("mouseout", () => {
1029
- config_btn.style("text-decoration", "none");
1030
- });
1031
- obj.menu_output = panel.append("div").style("margin-top", "10px").style("display", obj.menu_minimized ? "none" : "block");
1032
- obj.show_zoom = true;
1033
- }
1034
- function render_controlpanel(obj, data) {
1035
- obj.menu_output.selectAll("*").remove();
1036
- if (data.category2color) {
1037
- const top_row = obj.menu_output.append("div").style("margin", "2px");
1038
- 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", () => {
1039
- if (select_all_checkbox.node().checked) {
1040
- obj.cells.categories[obj.use_category_index].hidden_types = [];
1041
- pcd_pipeline(obj);
1042
- } else {
1043
- for (const type in data.category2color) {
1044
- obj.cells.categories[obj.use_category_index].hidden_types.push(type);
1045
- }
1046
- pcd_pipeline(obj);
1047
- }
1048
- });
1049
- if (obj.cells.categories[obj.use_category_index].hidden_types.length == 0) {
1050
- select_all_checkbox.property("checked", 1);
1051
- }
1052
- top_row.append("span").text("Select All").style("font-size", ".8em").attr("font-family", font);
1053
- for (const type in data.category2color) {
1054
- const row = obj.menu_output.append("div").style("margin", "2px");
1055
- 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", () => {
1056
- if (obj.cells.categories[obj.use_category_index].hidden_types.includes(type)) {
1057
- const index = obj.cells.categories[obj.use_category_index].hidden_types.indexOf(type);
1058
- if (index !== -1) obj.cells.categories[obj.use_category_index].hidden_types.splice(index, 1);
1059
- checkbox.property("checked", 1);
1060
- } else {
1061
- obj.cells.categories[obj.use_category_index].hidden_types.push(type);
1062
- }
1063
- pcd_pipeline(obj);
1064
- });
1065
- if (obj.cells.categories[obj.use_category_index].hidden_types.includes(type)) {
1066
- checkbox.property("checked", 0);
1067
- }
1068
- row.append("div").style("display", "inline-block").style("height", "15px").style("width", "15px").style("background-color", data.category2color[type]).style("margin-right", "10px");
1069
- row.append("span").text(type).attr("font-family", font);
1070
- row.append("span").html("&nbsp;n=" + data.categorycount[type]).attr("font-family", font).style("font-size", ".8em").style("float", "right").style("color", "#777");
1071
- }
1072
- } else if (data.maxexpvalue) {
1073
- const scale_height = 30;
1074
- const scale_width = 150;
1075
- const scale_div = obj.menu_output.append("div").style("margin", "10px").style("width", "120px").style("height", "100px");
1076
- scale_div.append("div").text("Gene Expression " + obj.gene_expression.datatype).style("text-align", "center").style("width", "150px").style("margin-bottom", "20px");
1077
- const svg = scale_div.append("svg").append("g");
1078
- const colorRange = [obj.gene_expression.color_max, obj.gene_expression.color_min];
1079
- const colorScale = linear().range(colorRange).domain([data.minexpvalue, data.maxexpvalue]);
1080
- const defs = svg.append("defs");
1081
- const linearGradient = defs.append("linearGradient").attr("id", "linear-gradient");
1082
- linearGradient.append("stop").attr("offset", "0%").attr("stop-color", colorScale(data.maxexpvalue));
1083
- linearGradient.append("stop").attr("offset", "100%").attr("stop-color", colorScale(data.minexpvalue));
1084
- 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)");
1085
- const y = linear().range([0, scale_width]).domain([data.minexpvalue, data.maxexpvalue]);
1086
- const legendAxis = axisBottom().scale(y).ticks(5);
1087
- svg.append("g").attr("class", "legend axis").attr("transform", "translate(12," + scale_height + ")").call(legendAxis);
1088
- const stats_div = obj.menu_output.append("div").style("padding-bottom", "20px").style("text-align", "center");
1089
- stats_div.append("p").style("font-size", "13px").style("margin", "2px 0").html("<b>Cells with Expression Data</b> ");
1090
- stats_div.append("p").style("font-size", "13px").style("margin", "2px 0").html(data.numbercellwithgeneexp + " / " + data.numbercelltotal);
1091
- const no_exp_div = stats_div.append("div").style("display", "block").style("margin-top", "10px");
1092
- 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");
1093
- no_exp_div.append("div").style("display", "inline-block").style("font-size", "13px").html(" Cells without Expression");
1094
- const boxplot_div = obj.menu_output.append("div");
1095
- boxplot_div.append("div").style("display", "block").style("padding", "5px").html("Violinplot / Boxplot of </br> Expression by");
1096
- const boxplot_cat_select = boxplot_div.append("select").style("display", "block");
1097
- boxplot_cat_select.append("option").attr("value", "none").text("-- Select--");
1098
- if (obj.cells.categories) {
1099
- obj.cells.categories.forEach((category, i) => {
1100
- boxplot_cat_select.append("option").attr("value", category.columnidx).text(category.name);
1101
- });
1102
- }
1103
- boxplot_cat_select.on("change", () => {
1104
- const gene = obj.gene_expression.genes[obj.use_gene_index];
1105
- const cat = obj.cells.categories[parseInt(boxplot_cat_select.node().selectedIndex) - 1];
1106
- const arg = {
1107
- genome: obj.genome.name,
1108
- getgeneboxplot: {
1109
- expfile: obj.gene_expression.file,
1110
- chr: gene.chr,
1111
- start: gene.start,
1112
- stop: gene.stop,
1113
- genename: gene.gene,
1114
- cellfile: obj.cells.file,
1115
- barcodecolumnidx: obj.cells.barcodecolumnidx,
1116
- categorycolumnidx: parseInt(boxplot_cat_select.node().value),
1117
- delimiter: obj.cells.delimiter || " ",
1118
- category_customorder: cat.customorder && cat.values ? true : false,
1119
- category_autoorder: !cat.customorder ? true : false,
1120
- cat_values: cat.values,
1121
- values_count: cat.values_count
1122
- }
1123
- };
1124
- dofetch("singlecell", arg).then((data2) => {
1125
- if (data2.error) throw data2.error;
1126
- obj.box_plot = new Menu();
1127
- make_plot(data2, obj, boxplot_cat_select.node().value);
1128
- });
1129
- });
1130
- }
1131
- make_zoom_panel(obj);
1132
- }
1133
- function make_zoom_panel(obj) {
1134
- if (obj.show_zoom) {
1135
- 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");
1136
- 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", () => {
1137
- zoom_div.node().remove();
1138
- obj.show_zoom = false;
1139
- }).on("mouseover", () => {
1140
- zoom_hide_btn.style("text-decoration", "underline");
1141
- }).on("mouseout", () => {
1142
- zoom_hide_btn.style("text-decoration", "none");
1143
- });
1144
- 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", () => {
1145
- obj.camera.fov = parseInt(obj.zoom_slider.node().value);
1146
- obj.camera.updateProjectionMatrix();
1147
- }).on("mousedown", (event) => {
1148
- event.stopPropagation();
1149
- });
1150
- }
1151
- }
1152
- function make_menu(obj) {
1153
- obj.menu.clear().showunder(obj.menu_button.node());
1154
- if (obj.cells.categories) {
1155
- obj.cells.categories.forEach((category, i) => {
1156
- if (i != obj.use_category_index) {
1157
- obj.menu.d.append("div").text(category.name).attr("class", "sja_menuoption").on("click", async () => {
1158
- obj.menu.hide();
1159
- obj.use_category_index = i;
1160
- pcd_pipeline(obj);
1161
- }).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 : "");
1162
- }
1163
- });
1164
- }
1165
- if (obj.gene_expression) {
1166
- obj.menu.d.append("div").text("Gene expression").attr("class", "sja_menuoption").on("click", () => {
1167
- obj.menu.clear();
1168
- const gene_search_div = obj.menu.d.append("div").style("padding", "10px");
1169
- gene_searchbox({
1170
- div: gene_search_div.append("div"),
1171
- resultdiv: gene_search_div.append("div"),
1172
- genome: obj.genome.name,
1173
- callback: async (genename) => {
1174
- const gmlst = await findgenemodel_bysymbol(obj.genome.name, genename);
1175
- if (gmlst && gmlst[0]) {
1176
- const gm = gmlst[0];
1177
- if (!obj.gene_expression.genes) obj.gene_expression.genes = [];
1178
- const geneidx = obj.gene_expression.genes.findIndex((i) => i.gene == genename);
1179
- if (geneidx == -1) {
1180
- obj.gene_expression.genes.push({
1181
- gene: genename,
1182
- chr: gm.chr,
1183
- start: gm.start,
1184
- stop: gm.stop
1185
- });
1186
- obj.use_gene_index = obj.gene_expression.genes.length - 1;
1187
- } else {
1188
- obj.use_gene_index = geneidx;
1189
- }
1190
- }
1191
- obj.use_category_index = null;
1192
- obj.menu.hide();
1193
- pcd_pipeline(obj);
1194
- }
1195
- });
1196
- });
1197
- obj.menu.d.append("div").text("Multi-Gene Heatmap").attr("class", "sja_menuoption").on("click", () => {
1198
- heatmap_menu(obj);
1199
- });
1200
- if (obj.gene_expression.genes) {
1201
- if (obj.gene_expression.genes.length > 1) {
1202
- obj.menu.d.append("div").style("padding", "5px 10px").text("Previously Selected");
1203
- }
1204
- obj.gene_expression.genes.forEach((gene, i) => {
1205
- if (i != obj.use_gene_index) {
1206
- obj.menu.d.append("div").text("Gene : " + gene.gene).attr("class", "sja_menuoption").on("click", async () => {
1207
- obj.menu.hide();
1208
- obj.use_category_index = null;
1209
- obj.use_gene_index = i;
1210
- pcd_pipeline(obj);
1211
- });
1212
- }
1213
- });
1214
- }
1215
- }
1216
- }
1217
- function make_settings(obj) {
1218
- obj.settings.clear().showunder(obj.settings_btn.node());
1219
- const back_color_div = obj.settings.d.append("div").style("display", "block").text("Background Color").style("margin", "5px");
1220
- const black_div = back_color_div.append("div").style("margin", "5px").style("display", "block");
1221
- const name = Math.random(), idblack = Math.random(), idwhite = Math.random();
1222
- const inputblack = black_div.append("input").attr("type", "radio").style("display", "inline-block").attr("name", name).attr("id", idblack).on("change", toggle_background);
1223
- black_div.append("label").style("display", "inline-block").style("font-size", ".8em").text("Black").style("padding-left", "10px").attr("for", idblack);
1224
- const white_div = back_color_div.append("div").style("margin", "5px").style("display", "block");
1225
- const inputwhite = white_div.append("input").attr("type", "radio").style("display", "inline-block").attr("name", name).attr("id", idwhite).on("change", toggle_background);
1226
- white_div.append("label").style("display", "inline-block").style("font-size", ".8em").text("White").style("padding-left", "10px").attr("for", idwhite);
1227
- if (obj.use_background_color == 0) {
1228
- inputwhite.property("checked", 1);
1229
- } else {
1230
- inputblack.property("checked", 1);
1231
- }
1232
- function toggle_background() {
1233
- const isblack = obj.background_color == "black";
1234
- obj.scene.background = new Color(isblack ? 16777215 : 0);
1235
- obj.use_background_color = isblack ? 0 : 1;
1236
- obj.background_color = isblack ? "white" : "black";
1237
- }
1238
- const point_size_div = obj.settings.d.append("div").style("display", "block").text("Point Size").style("margin", "20px 5px");
1239
- 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", () => {
1240
- obj.scene.children[1].material.size = point_size_slider.node().value / 100;
1241
- });
1242
- if (obj.show_zoom == false) {
1243
- const zoom_div = obj.settings.d.append("div").style("display", "block").text("Zoom").style("margin", "20px 5px");
1244
- 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", () => {
1245
- zoom_div.node().remove();
1246
- obj.show_zoom = true;
1247
- make_zoom_panel(obj);
1248
- }).on("mouseover", () => {
1249
- zoom_hide_btn.style("text-decoration", "underline");
1250
- }).on("mouseout", () => {
1251
- zoom_hide_btn.style("text-decoration", "none");
1252
- });
1253
- 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", () => {
1254
- obj.camera.fov = parseInt(obj.zoom_slider.node().value);
1255
- obj.camera.updateProjectionMatrix();
1256
- });
1257
- }
1258
- obj.settings.d.append("div").style("margin", "5px").text("Panning");
1259
- 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>');
1260
- if (!obj.canvas_2d) {
1261
- obj.settings.d.append("div").style("margin", "5px").text("Rotate");
1262
- 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>');
1263
- }
1264
- 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", () => {
1265
- inputwhite.property("checked", 1);
1266
- obj.scene.background = new Color(obj.background_color ? obj.background_color : 16777215);
1267
- point_size_slider.node().value = obj.point_size ? obj.point_size * 100 : obj.canvas_2d ? 30 : 5;
1268
- obj.scene.children[1].material.size = obj.point_size ? obj.point_size : obj.canvas_2d ? 0.3 : 0.05;
1269
- obj.camera.position.z = obj.data_sphere_r * 3;
1270
- obj.camera.position.x = obj.canvas_2d ? 0 : 20;
1271
- obj.camera.position.y = obj.canvas_2d ? 0 : -10;
1272
- const cam_fov_default = 45;
1273
- obj.camera.fov = parseInt(cam_fov_default);
1274
- obj.camera.updateProjectionMatrix();
1275
- obj.zoom_slider.node().value = cam_fov_default;
1276
- if (obj.canvas_2d) {
1277
- obj.camera.up.set(0, 1, 0);
1278
- } else {
1279
- obj.camera.up.set(0, 0, 1);
1280
- }
1281
- obj.controls.target.set(obj.center.x, obj.center.y, obj.center.z);
1282
- });
1283
- 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", () => {
1284
- const imgData = obj.renderer.domElement.toDataURL();
1285
- let imgNode = document.createElement("img");
1286
- imgNode.src = imgData;
1287
- screenshot_btn.append("span").style("display", "none").html(
1288
- '<a download="scRNA_' + (/* @__PURE__ */ new Date()).toLocaleString() + '.png" href="' + imgNode.src + '" title="ImageName">Camera</a>'
1289
- );
1290
- }).on("mouseup", () => {
1291
- screenshot_btn.select("a").node().click();
1292
- screenshot_btn.selectAll("span").remove();
1293
- });
1294
- }
1295
- function heatmap_menu(obj) {
1296
- obj.menu.clear();
1297
- obj.gene_expression.heatmap_genes = [];
1298
- obj.use_heatmap_category_index = null;
1299
- const heatmap_menu_div = obj.menu.d.append("div").style("display", "block").style("padding", "10px");
1300
- const genes_div = heatmap_menu_div.append("div").style("display", "block");
1301
- const gene_search_div = genes_div.append("div").style("display", "inline-block").style("vertical-align", "top").style("padding", "10px");
1302
- gene_search_div.append("div").style("display", "block").style("padding-bottom", "5px").text("Add Genes");
1303
- gene_search_div.append("textarea").attr("rows", "4").attr("cols", "20").attr("placeholder", "Type gene names seperated by space");
1304
- const catagory_div = heatmap_menu_div.append("div");
1305
- catagory_div.append("div").style("display", "block").style("padding-bottom", "5px").style("padding-left", "10px").text("Heatmap by");
1306
- const cat_select = catagory_div.append("select").style("display", "block").style("margin-left", "10px");
1307
- cat_select.append("option").attr("value", "none").text("-- Select--");
1308
- if (obj.cells.categories) {
1309
- obj.cells.categories.forEach((category, i) => {
1310
- cat_select.append("option").attr("value", category.columnidx).text(category.name);
1311
- });
1312
- }
1313
- cat_select.on("change", () => {
1314
- obj.use_heatmap_category_index = parseInt(cat_select.node().value);
1315
- });
1316
- heatmap_menu_div.append("button").text("Heatmap").style("display", "block").style("float", "right").style("margin", "5px").on("click", async () => {
1317
- const input_genelist = gene_search_div.select("textarea").node().value;
1318
- const genelist = input_genelist.split(" ");
1319
- for (const gene of genelist) {
1320
- const gmlst = await findgenemodel_bysymbol(obj.genome.name, gene);
1321
- if (gmlst && gmlst[0]) {
1322
- const gm = gmlst[0];
1323
- if (!obj.gene_expression.heatmap_genes) obj.gene_expression.heatmap_genes = [];
1324
- const geneidx = obj.gene_expression.heatmap_genes.findIndex((i) => i.gene == gene);
1325
- if (geneidx == -1) {
1326
- obj.gene_expression.heatmap_genes.push({
1327
- gene,
1328
- chr: gm.chr,
1329
- start: gm.start,
1330
- stop: gm.stop
1331
- });
1332
- }
1333
- }
1334
- }
1335
- const arg = {
1336
- genome: obj.genome.name,
1337
- getheatmap: {
1338
- expfile: obj.gene_expression.file,
1339
- gene_list: obj.gene_expression.heatmap_genes,
1340
- cellfile: obj.cells.file,
1341
- barcodecolumnidx: obj.cells.barcodecolumnidx,
1342
- categorycolumnidx: parseInt(cat_select.node().value),
1343
- delimiter: obj.cells.delimiter || " "
1344
- }
1345
- };
1346
- dofetch("singlecell", arg).then((data) => {
1347
- if (data.error) throw data.error;
1348
- obj.menu.hide();
1349
- make_heatmap(data, obj, cat_select.node().value);
1350
- });
1351
- });
1352
- }
1353
- function make_plot(data, obj, colidx) {
1354
- const gene = obj.gene_expression.genes[obj.use_gene_index];
1355
- const pane = newpane({ x: 600, y: 400 });
1356
- const cat = obj.cells.categories.find((x) => x.columnidx == colidx);
1357
- pane.header.text("Violinplot/Boxplot for " + gene.gene + " Expression by " + cat.name);
1358
- const control_panel = pane.pane.append("div").style("margin", "10px 10px 10px 15px");
1359
- const svg = pane.pane.append("svg").style("margin", "10px");
1360
- const plot_select = control_panel.append("select").style("display", "inline-block");
1361
- plot_select.append("option").attr("value", "violin").text("Violin Plot");
1362
- plot_select.append("option").attr("value", "box").text("Box Plot");
1363
- plot_select.on("change", () => {
1364
- apply();
1365
- });
1366
- const cell_select_div = control_panel.append("div").style("display", "inline-block").style("padding-left", "15px").text("Cells without expression");
1367
- const cell_select = cell_select_div.append("select").style("display", "inline-block").style("margin-left", "5px");
1368
- cell_select.append("option").attr("value", "include").text("Include");
1369
- cell_select.append("option").attr("value", "exclude").text("Exclude");
1370
- cell_select.on("change", () => {
1371
- apply();
1372
- });
1373
- make_violin_plot(data, svg);
1374
- function apply() {
1375
- const gene2 = obj.gene_expression.genes[obj.use_gene_index];
1376
- const arg = {
1377
- genome: obj.genome.name,
1378
- getgeneboxplot: {
1379
- expfile: obj.gene_expression.file,
1380
- chr: gene2.chr,
1381
- start: gene2.start,
1382
- stop: gene2.stop,
1383
- genename: gene2.gene,
1384
- cellfile: obj.cells.file,
1385
- barcodecolumnidx: obj.cells.barcodecolumnidx,
1386
- categorycolumnidx: parseInt(colidx),
1387
- delimiter: obj.cells.delimiter || " ",
1388
- category_customorder: cat.customorder && cat.values ? true : false,
1389
- category_autoorder: !cat.customorder ? true : false,
1390
- cat_values: cat.values,
1391
- values_count: cat.values_count
1392
- }
1393
- };
1394
- if (cell_select.node().value == "exclude") {
1395
- arg.getgeneboxplot.exclude_cells = true;
1396
- }
1397
- dofetch("singlecell", arg).then((data2) => {
1398
- if (data2.error) throw data2.error;
1399
- if (plot_select.node().value == "box") make_box_plot(data2, svg);
1400
- else if (plot_select.node().value == "violin") make_violin_plot(data2, svg);
1401
- });
1402
- }
1403
- }
1404
- function make_violin_plot(data, svg) {
1405
- svg.selectAll("*").remove();
1406
- let box_height = 50, box_width = 200, barspace = 2, axis_height = 30;
1407
- const label_width = get_max_labelwidth(data.boxplots, svg);
1408
- const x_scale = linear().range([0, box_width]).domain([data.minexpvalue, data.maxexpvalue]);
1409
- const y_scale = linear().range([box_height, 0]).domain([0, 1]);
1410
- const svg_height = data.boxplots.length * (box_height + barspace) + axis_height;
1411
- const svg_width = box_width + label_width + 20;
1412
- svg.transition().attr("width", svg_width).attr("height", svg_height);
1413
- if (data.boxplots) {
1414
- data.boxplots.forEach((boxplot, i) => {
1415
- const g = svg.append("g").attr("transform", "translate(" + label_width + "," + (i * (box_height + barspace) + axis_height) + ")");
1416
- 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");
1417
- if (boxplot.density) {
1418
- const density_max = Math.max(...boxplot.density);
1419
- const line = line_default().x(function(d, j) {
1420
- return x_scale(j * data.maxexpvalue / boxplot.density.length);
1421
- }).y(function(d) {
1422
- return y_scale(d / density_max) / 2;
1423
- }).curve(monotoneX);
1424
- const area = area_default().x(function(d, j) {
1425
- return x_scale(j * data.maxexpvalue / boxplot.density.length);
1426
- }).y0(function(d) {
1427
- const temp = y_scale(d / density_max) / 2;
1428
- return box_height - temp;
1429
- }).y1(function(d) {
1430
- return y_scale(d / density_max) / 2;
1431
- }).curve(monotoneX);
1432
- g.append("path").datum(boxplot.density).attr("class", "area").attr("d", area).style("fill", boxplot.color).style("stroke", "black").style("stroke-width", 0.5);
1433
- }
1434
- });
1435
- const legendAxis = axisTop().scale(x_scale).ticks(5);
1436
- svg.append("g").attr("class", "legend axis").attr("transform", "translate(" + label_width + "," + (axis_height - 10) + ")").call(legendAxis);
1437
- }
1438
- }
1439
- function make_box_plot(data, svg) {
1440
- svg.selectAll("*").remove();
1441
- let box_height = 36, box_width = 200, barspace = 16, axis_height = 30;
1442
- const label_width = get_max_labelwidth(data.boxplots, svg);
1443
- const x_scale = linear().range([0, box_width]).domain([data.minexpvalue, data.maxexpvalue]);
1444
- const y_scale = linear().range([box_height, 0]).domain([0, 1]);
1445
- const svg_height = data.boxplots.length * (box_height + barspace) + axis_height;
1446
- const svg_width = box_width + label_width + 20;
1447
- svg.transition().attr("width", svg_width).attr("height", svg_height);
1448
- if (data.boxplots) {
1449
- data.boxplots.forEach((boxplot, i) => {
1450
- const g = svg.append("g").attr("transform", "translate(" + label_width + "," + (i * (box_height + barspace) + axis_height) + ")");
1451
- 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");
1452
- if (boxplot.p75) {
1453
- 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");
1454
- 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);
1455
- 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");
1456
- 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");
1457
- 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");
1458
- if (boxplot.out) {
1459
- for (const outlier of boxplot.out) {
1460
- g.append("circle").attr("cx", x_scale(outlier.value)).attr("cy", box_height / 2).attr("r", 2).attr("fill", "#901739");
1461
- }
1462
- }
1463
- }
1464
- });
1465
- const legendAxis = axisTop().scale(x_scale).ticks(5);
1466
- svg.append("g").attr("class", "legend axis").attr("transform", "translate(" + label_width + "," + (axis_height - 10) + ")").call(legendAxis);
1467
- }
1468
- }
1469
- function make_heatmap(data, obj, colidx) {
1470
- const pane = newpane({ x: 600, y: 400 });
1471
- const cat = obj.cells.categories.find((x) => x.columnidx == colidx);
1472
- pane.header.text("Heatmap for Gene Expression by " + cat.name);
1473
- const svg = pane.pane.append("svg").style("margin", "10px");
1474
- let gene_list = [];
1475
- for (const gene of data.gene_heatmap) gene_list.push(gene.genename);
1476
- let means = [];
1477
- data.gene_heatmap.forEach((gene, i) => {
1478
- data.gene_heatmap[i].heatmap.forEach((category) => {
1479
- means.push(category.mean);
1480
- });
1481
- });
1482
- const max_mean = Math.max(...means);
1483
- let categories = [];
1484
- for (const category of data.gene_heatmap[0].heatmap)
1485
- categories.push(category.category + " (" + category.numberofcells + ")");
1486
- let box_height = 20, box_width = 80, barspace = 2, gene_lable_height = 30, legend_width = 60;
1487
- const label_width = get_max_labelwidth(data.gene_heatmap[0].heatmap, svg);
1488
- const svg_height = (box_height + barspace) * categories.length + gene_lable_height;
1489
- const svg_width = (box_width + barspace) * gene_list.length + label_width + legend_width + 20;
1490
- svg.transition().attr("width", svg_width).attr("height", svg_height);
1491
- const x_scale = band().range([0, (box_width + barspace) * gene_list.length]).domain(gene_list).padding(0.05);
1492
- svg.append("g").style("font-size", 15).attr("transform", "translate(" + label_width + ",0)").call(axisBottom(x_scale).tickSize(0)).select(".domain").remove();
1493
- const y_scale = band().range([(box_height + barspace) * categories.length, 0]).domain(categories).padding(0.05);
1494
- svg.append("g").style("font-size", 15).attr("transform", "translate(" + label_width + "," + gene_lable_height + ")").call(axisLeft(y_scale).tickSize(0)).select(".domain").remove();
1495
- var myColor = sequential().interpolator(plasma).domain([0, max_mean]);
1496
- 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);
1497
- data.gene_heatmap.forEach((gene, i) => {
1498
- data.gene_heatmap[i].heatmap.forEach((category, j) => {
1499
- const g = svg.append("g").attr("transform", "translate(" + label_width + "," + gene_lable_height + ")");
1500
- 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) {
1501
- div.transition().duration(200).style("opacity", 0.9);
1502
- div.html("Mean Expression: " + category.mean).style("left", pointer_default(event, this)[0] + 70 + "px").style("top", pointer_default(event, this)[1] + 20 + "px");
1503
- }).on("mouseout", function() {
1504
- div.transition().duration(500).style("opacity", 0);
1505
- });
1506
- });
1507
- });
1508
- const legend_data = myColor.ticks(10).reverse();
1509
- legend_data.unshift(max_mean.toFixed(2));
1510
- const legend = svg.selectAll(".legend").data(legend_data).enter().append("g").attr("class", "legend").attr("transform", function(d, i) {
1511
- return "translate(" + (svg_width - legend_width) + "," + (30 + i * 20) + ")";
1512
- });
1513
- legend.append("rect").attr("width", 20).attr("height", 20).style("fill", myColor).style("opacity", 0.8);
1514
- legend.append("text").attr("x", 26).attr("y", 10).attr("dy", ".35em").text(String);
1515
- }
1516
- function get_max_labelwidth(items, svg) {
1517
- let textwidth = 0;
1518
- for (const i of items) {
1519
- svg.append("text").text(i.category + " (" + i.numberofcells + ")").attr("font-family", font).attr("font-size", 15).each(function() {
1520
- textwidth = Math.max(textwidth, this.getBBox().width);
1521
- }).remove();
1522
- }
1523
- return textwidth + 4;
1524
- }
1525
- async function make_legend(arg, obj) {
1526
- if (!arg.legendimg) return;
1527
- const img_div = obj.holder.append("div").style("margin-top", "5px");
1528
- obj.legendimg = arg.legendimg;
1529
- obj.legend = {
1530
- holder: img_div,
1531
- legendcolor: "#7D6836"
1532
- };
1533
- let shown = !arg.foldlegend;
1534
- 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", () => {
1535
- if (shown) {
1536
- shown = false;
1537
- disappear(div2);
1538
- } else {
1539
- shown = true;
1540
- appear(div2);
1541
- }
1542
- });
1543
- const div2 = obj.holder.append("div").style("border-top", "solid 1px " + obj.legend.legendcolor).style("background-color", "#FCFBF7");
1544
- obj.legend.holder = div2.append("table").style("border-spacing", "15px").style("border-collapse", "separate");
1545
- const [tr, td] = legend_newrow(obj, obj.legendimg.name || "");
1546
- const data = await dofetch2("img?file=" + obj.legendimg.file);
1547
- if (data.error) {
1548
- td.text(data.error);
1549
- return;
1550
- }
1551
- let fold = true;
1552
- const img = td.append("img").attr("class", "sja_clbb").attr("src", data.src).style("height", "80px");
1553
- img.on("click", () => {
1554
- if (fold) {
1555
- fold = false;
1556
- img.transition().style("height", obj.legendimg.height ? obj.legendimg.height + "px" : "auto");
1557
- } else {
1558
- fold = true;
1559
- img.transition().style("height", "80px");
1560
- }
1561
- });
1562
- }
1563
- export {
1564
- init
1565
- };
1566
- //# sourceMappingURL=singlecell-UKN2VCXQ.js.map