@sjcrh/proteinpaint-client 2.166.0 → 2.167.0

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 (882) hide show
  1. package/dist/2dmaf-VLW5XJ4O.js +1364 -0
  2. package/dist/AIProjectAdmin-X3TBCRPR.js +780 -0
  3. package/dist/AppHeader-YA7FCKVM.js +813 -0
  4. package/dist/BoxPlot-PAZYARCX.js +44 -0
  5. package/dist/CorrelationVolcano-S35GWKV5.js +616 -0
  6. package/dist/DifferentialAnalysis-DTDFAUXT.js +237 -0
  7. package/dist/Disco-OE6YY3MH.js +3089 -0
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  823. /package/dist/{profile.spec-A6EADWEC.js.map → profile.spec-DOQYKG6P.js.map} +0 -0
  824. /package/dist/{profileBarchart-EFLPJK2P.js.map → profileBarchart-A4UWV2YA.js.map} +0 -0
  825. /package/dist/{profileForms-TG35YNLD.js.map → profileForms-VONTWVOF.js.map} +0 -0
  826. /package/dist/{profilePlot-2EW2XVTK.js.map → profilePlot-OK5VKWO4.js.map} +0 -0
  827. /package/dist/{profileRadar-AKUYC2O5.js.map → profileRadar-VLEZJCD7.js.map} +0 -0
  828. /package/dist/{profileRadarFacility-EAT66XTX.js.map → profileRadarFacility-QPSSUTB6.js.map} +0 -0
  829. /package/dist/{qualitative-PHQU5DXE.js.map → qualitative-RJKAWHQR.js.map} +0 -0
  830. /package/dist/{regression-EOMJRRDO.js.map → regression-GV73BYCQ.js.map} +0 -0
  831. /package/dist/{regression.inputs-LIH5X2JM.js.map → regression.inputs-PVIJHCRE.js.map} +0 -0
  832. /package/dist/{regression.inputs.term-OO4RZ3QB.js.map → regression.inputs.term-V5I3EP6M.js.map} +0 -0
  833. /package/dist/{regression.inputs.values.table-E7WCTO2L.js.map → regression.inputs.values.table-Y37EJUQB.js.map} +0 -0
  834. /package/dist/{regression.integration.spec-62VEQP6X.js.map → regression.integration.spec-JD32ODD2.js.map} +0 -0
  835. /package/dist/{regression.results-WAHFJ6NA.js.map → regression.results-AHAYXYGI.js.map} +0 -0
  836. /package/dist/{regression.spec-IBIOTZVX.js.map → regression.spec-FGYEES5G.js.map} +0 -0
  837. /package/dist/{report-MKDJXHGY.js.map → report-JYIEDDW5.js.map} +0 -0
  838. /package/dist/{runChart-ETM2EETF.js.map → runChart-CVAWIBA3.js.map} +0 -0
  839. /package/dist/{runchart.integration.spec-QFA4XBKB.js.map → runchart.integration.spec-5Z4IHQU5.js.map} +0 -0
  840. /package/dist/{sampleScatter.spec-N4N7ZGZF.js.map → sampleScatter.spec-QNFWS2Y7.js.map} +0 -0
  841. /package/dist/{sampleView-JTY3RV7I.js.map → sampleView-GKYHS3WO.js.map} +0 -0
  842. /package/dist/{samplelst-RRUMBVT6.js.map → samplelst-CHBS5BGY.js.map} +0 -0
  843. /package/dist/{samplematrix-L37O664Y.js.map → samplematrix-IK4YDAID.js.map} +0 -0
  844. /package/dist/{scatter-E5QHW32W.js.map → scatter-NDA5YSCP.js.map} +0 -0
  845. /package/dist/{scatter.integration.spec-FNVAJSVU.js.map → scatter.integration.spec-GV3EIFGT.js.map} +0 -0
  846. /package/dist/{selectGenomeWithTklst-J6VXCYGG.js.map → selectGenomeWithTklst-X7RAGKRC.js.map} +0 -0
  847. /package/dist/{singleCellPlot-S6S6CKYX.js.map → singleCellPlot-7F735HTR.js.map} +0 -0
  848. /package/dist/{singlecell-B4TNI23F.js.map → singlecell-EO3WYGS7.js.map} +0 -0
  849. /package/dist/{singlecell-4BMIKFY4.js.map → singlecell-YMYLKTSC.js.map} +0 -0
  850. /package/dist/{snp-PAUQ24NZ.js.map → snp-6KN4AWBB.js.map} +0 -0
  851. /package/dist/{snplocus-HVFYZTEE.js.map → snplocus-CLM4WHVH.js.map} +0 -0
  852. /package/dist/{spliceevent.a53ss.diagram-GGGHVNBF.js.map → spliceevent.a53ss.diagram-PKFVC2N4.js.map} +0 -0
  853. /package/dist/{spliceevent.exonskip.diagram-HLMFD6LJ.js.map → spliceevent.exonskip.diagram-XV2Z7AYB.js.map} +0 -0
  854. /package/dist/{spliceevent.noeventdiagram-CKZ3BZ7Y.js.map → spliceevent.noeventdiagram-L5L2BJL5.js.map} +0 -0
  855. /package/dist/{ssGSEA-UGT4GH55.js.map → ssGSEA-W6N4CXMD.js.map} +0 -0
  856. /package/dist/{stattable-6JWMALGB.js.map → stattable-324FS2HA.js.map} +0 -0
  857. /package/dist/{summarizeCnvGeneexp-BJOQY62E.js.map → summarizeCnvGeneexp-57LZ5B2Q.js.map} +0 -0
  858. /package/dist/{summarizeGeneexpSurvival-4HDHL7PE.js.map → summarizeGeneexpSurvival-UQX3VZUK.js.map} +0 -0
  859. /package/dist/{summarizeMutationDiagnosis-TDWO5CKU.js.map → summarizeMutationDiagnosis-5SWO42E4.js.map} +0 -0
  860. /package/dist/{summarizeMutationSurvival-CJJFABOX.js.map → summarizeMutationSurvival-EOU5QOB6.js.map} +0 -0
  861. /package/dist/{summary-WOAXXIHG.js.map → summary-FRIKVPYZ.js.map} +0 -0
  862. /package/dist/{summary.integration.spec-GM73ERMN.js.map → summary.integration.spec-WSI3JNTO.js.map} +0 -0
  863. /package/dist/{summaryInput-FD4SONTY.js.map → summaryInput-3L7CM52X.js.map} +0 -0
  864. /package/dist/{sunburst-3LCJTBRN.js.map → sunburst-HA7UGSXX.js.map} +0 -0
  865. /package/dist/{survival-A3A7IVXT.js.map → survival-2HZ446Y3.js.map} +0 -0
  866. /package/dist/{survival-XF72VMM6.js.map → survival-LJI5JEZZ.js.map} +0 -0
  867. /package/dist/{survival.integration.spec-AU7MCAQV.js.map → survival.integration.spec-7XVO2WNF.js.map} +0 -0
  868. /package/dist/{svgraph-BEMS4JDJ.js.map → svgraph-TRPAXTNP.js.map} +0 -0
  869. /package/dist/{svmr-CDEMTZPK.js.map → svmr-TJOCKTE2.js.map} +0 -0
  870. /package/dist/{table-WYF6QCGB.js.map → table-35RHJK4M.js.map} +0 -0
  871. /package/dist/{termCollection-BVQMNVY7.js.map → termCollection-JS6N5TAP.js.map} +0 -0
  872. /package/dist/{termInfo-JXLIVCSO.js.map → termInfo-5USFZGDB.js.map} +0 -0
  873. /package/dist/{tk-TGIIJYBO.js.map → tk-4ARNGTEQ.js.map} +0 -0
  874. /package/dist/{tp.ui-USYF67P7.js.map → tp.ui-QZEMGVEH.js.map} +0 -0
  875. /package/dist/{tvs.dtcnv.continuous-7SCTSFK3.js.map → tvs.dtcnv.continuous-4K7B7FXF.js.map} +0 -0
  876. /package/dist/{tvs.numeric-OLVW6US3.js.map → tvs.numeric-FCC2EY62.js.map} +0 -0
  877. /package/dist/{tvs.samplelst-BHZHCX5V.js.map → tvs.samplelst-IUSDLB6P.js.map} +0 -0
  878. /package/dist/{violin-OEOWVIZF.js.map → violin-I5JO56GZ.js.map} +0 -0
  879. /package/dist/{violin.integration.spec-AW2U3RHO.js.map → violin.integration.spec-5WVLT3DW.js.map} +0 -0
  880. /package/dist/{violin.interactivity-3O2UDNPQ.js.map → violin.interactivity-EFFBMTN2.js.map} +0 -0
  881. /package/dist/{violin.renderer-W26FA6M7.js.map → violin.renderer-Z3AIV5RH.js.map} +0 -0
  882. /package/dist/{vocabulary-BIQYDKVY.js.map → vocabulary-4PHACFSG.js.map} +0 -0
@@ -1,480 +0,0 @@
1
- import {
2
- Scatter,
3
- ScatterInteractivity
4
- } from "./chunk-ZHWC5SJP.js";
5
- import {
6
- ScatterModel,
7
- ScatterView,
8
- ScatterViewModelBase
9
- } from "./chunk-ETFPL4UP.js";
10
- import {
11
- controlsInit
12
- } from "./chunk-CZTC4MTE.js";
13
- import {
14
- fillTermWrapper,
15
- select2Terms
16
- } from "./chunk-UT6W4ZZL.js";
17
- import {
18
- getDateFromNumber,
19
- isNumericTerm
20
- } from "./chunk-RYRCMHYR.js";
21
- import {
22
- getColors,
23
- plotColor
24
- } from "./chunk-ECKWM4HB.js";
25
- import {
26
- copyMerge,
27
- getCompInit
28
- } from "./chunk-FYTZCTJC.js";
29
- import {
30
- line_default
31
- } from "./chunk-PMZS3SHH.js";
32
- import {
33
- median
34
- } from "./chunk-W2IWHXLL.js";
35
- import {
36
- roundValueAuto
37
- } from "./chunk-5OHXYXLD.js";
38
- import {
39
- rgb
40
- } from "./chunk-OMR2DT66.js";
41
-
42
- // plots/runchart/model/runchartModel.ts
43
- var RunchartModel = class extends ScatterModel {
44
- createChart(id, data) {
45
- const aggregate = this.scatter.settings.aggregateData;
46
- const samples = data.samples;
47
- if (aggregate !== "None") {
48
- const groupedSamples = /* @__PURE__ */ new Map();
49
- for (const sample of samples) {
50
- const date = new Date(getDateFromNumber(sample.x));
51
- const year = date.getFullYear();
52
- const month = date.getMonth() + 1;
53
- const key = `${year}-${month}`;
54
- if (!groupedSamples.has(key)) groupedSamples.set(key, { ysum: sample.y, xsum: sample.x, samples: [sample] });
55
- else {
56
- const value = groupedSamples.get(key);
57
- groupedSamples.set(key, {
58
- ysum: value.ysum + sample.y,
59
- xsum: value.xsum + sample.x,
60
- samples: [...value.samples, sample]
61
- });
62
- }
63
- }
64
- for (const value of groupedSamples.values()) {
65
- let x, y;
66
- if (aggregate == "Median") {
67
- x = median(value.samples.map((d) => d.x));
68
- y = median(value.samples.map((d) => d.y));
69
- } else if (aggregate == "Mean") {
70
- y = value.ysum / value.samples.length;
71
- x = value.xsum / value.samples.length;
72
- }
73
- for (const sample of value.samples) {
74
- sample.x = x;
75
- sample.y = y;
76
- }
77
- }
78
- }
79
- const colorLegend = new Map(data.colorLegend);
80
- const shapeLegend = new Map(data.shapeLegend);
81
- this.charts.push({ id, data, cohortSamples: samples, colorLegend, shapeLegend });
82
- }
83
- };
84
-
85
- // plots/runchart/viewmodel/runchartViewModel.ts
86
- var RunchartViewModel = class extends ScatterViewModelBase {
87
- constructor(runchart) {
88
- super(runchart);
89
- this.runchart = runchart;
90
- }
91
- render() {
92
- this.view.dom.mainDiv.select("svg").selectAll("*").remove();
93
- for (const chart of this.model.charts) this.renderChart(chart, this.view.dom.mainDiv, false);
94
- }
95
- renderSerie(chart, removePrevious) {
96
- super.renderSerie(chart, removePrevious);
97
- this.showRunChart(chart);
98
- }
99
- showRunChart(chart) {
100
- const g = chart.serie;
101
- const color = this.runchart.config.term0 ? this.runchart.cat2Color(chart.id) : this.runchart.settings.defaultColor;
102
- const coords = chart.cohortSamples.map((s) => this.model.getCoordinates(chart, s)).sort((a, b) => a.x - b.x);
103
- const medianColor = rgb(color).darker(2);
104
- const xtext = coords[coords.length - 1].x - 30;
105
- const areaBuilder = line_default().x((d) => d.x).y((d) => d.y);
106
- g.append("path").attr("stroke", color).attr("fill", "none").attr("stroke-width", 1).attr("stroke-linejoin", "round").attr("opacity", this.runchart.settings.opacity).attr("d", areaBuilder(coords));
107
- if (!this.scatter.settings.showCumulativeFrequency) {
108
- const median2 = median(chart.cohortSamples, (d) => d.y);
109
- const y = chart.yAxisScale(median2);
110
- g.append("line").attr("x1", coords[0].x).attr("y1", y).attr("x2", coords[coords.length - 1].x).attr("y2", y).attr("stroke", medianColor).attr("stroke-width", 1).attr("opacity", 0.5);
111
- g.append("text").attr("x", xtext).attr("y", y - 5).attr("text-anchor", "start").text("M=" + roundValueAuto(median2, true, 1)).attr("opacity", 0.8).attr("font-size", "0.8em").attr("fill", medianColor);
112
- }
113
- }
114
- };
115
-
116
- // plots/runchart/view/runchartView.ts
117
- var minShapeSize = 0.2;
118
- var maxShapeSize = 6;
119
- var RunchartView = class extends ScatterView {
120
- constructor(runchart) {
121
- super(runchart);
122
- this.runchart = runchart;
123
- }
124
- async getControlInputs() {
125
- const inputs = [];
126
- const shapeOption = {
127
- type: "term",
128
- configKey: "shapeTW",
129
- chartType: "runChart",
130
- usecase: { target: "runChart", detail: "shapeTW" },
131
- title: "Categories to assign a shape",
132
- label: "Shape",
133
- vocabApi: this.runchart.app.vocabApi,
134
- numericEditMenuVersion: ["discrete"],
135
- processInput: async (tw) => {
136
- if (isNumericTerm(tw?.term)) {
137
- tw.q = { mode: "discrete" };
138
- await fillTermWrapper(tw, this.runchart.app.vocabApi);
139
- }
140
- }
141
- };
142
- const shapeSizeOption = {
143
- label: "Sample size",
144
- type: "number",
145
- chartType: "runChart",
146
- settingsKey: "size",
147
- title: "Sample size, represents the factor used to scale the sample",
148
- min: 0,
149
- step: 0.1
150
- };
151
- const step = (maxShapeSize - minShapeSize) / 10;
152
- const minShapeSizeOption = {
153
- label: "Min size",
154
- type: "number",
155
- chartType: "runChart",
156
- settingsKey: "minShapeSize",
157
- title: "Minimum sample size",
158
- min: minShapeSize,
159
- max: maxShapeSize,
160
- step
161
- };
162
- const maxShapeSizeOption = {
163
- label: "Max size",
164
- type: "number",
165
- chartType: "runChart",
166
- settingsKey: "maxShapeSize",
167
- title: "Maximum sample size",
168
- min: minShapeSize,
169
- max: maxShapeSize * 2,
170
- step
171
- };
172
- inputs.push(
173
- ...[
174
- {
175
- type: "term",
176
- configKey: "term",
177
- chartType: "runChart",
178
- usecase: { target: "runChart", detail: "numeric" },
179
- title: "X coordinate to plot the samples",
180
- label: "X",
181
- vocabApi: this.runchart.app.vocabApi,
182
- menuOptions: "!remove",
183
- numericEditMenuVersion: ["continuous"]
184
- },
185
- {
186
- type: "term",
187
- configKey: "term2",
188
- chartType: "runChart",
189
- usecase: { target: "runChart", detail: "numeric" },
190
- title: "Y coordinate to plot the samples",
191
- label: "Y",
192
- vocabApi: this.runchart.app.vocabApi,
193
- menuOptions: "!remove",
194
- numericEditMenuVersion: ["continuous"]
195
- },
196
- {
197
- boxLabel: "",
198
- label: "Aggregate data",
199
- chartType: "runChart",
200
- settingsKey: "aggregateData",
201
- title: `Group samples from the same month and year`,
202
- type: "dropdown",
203
- options: [
204
- { label: "None", value: "None" },
205
- //{ label: 'Loess', value: 'Loess' },
206
- { label: "Median", value: "Median" },
207
- { label: "Mean", value: "Mean" }
208
- ]
209
- },
210
- {
211
- type: "term",
212
- configKey: "term0",
213
- chartType: "runChart",
214
- usecase: { target: "runChart", detail: "term0" },
215
- title: "Term to to divide by categories",
216
- label: "Divide by",
217
- vocabApi: this.runchart.app.vocabApi,
218
- numericEditMenuVersion: ["discrete"]
219
- },
220
- {
221
- type: "term",
222
- configKey: "colorTW",
223
- chartType: "runChart",
224
- usecase: { target: "runChart", detail: "colorTW" },
225
- title: "Categories to color the samples",
226
- label: "Color",
227
- vocabApi: this.runchart.app.vocabApi,
228
- numericEditMenuVersion: ["continuous", "discrete"]
229
- },
230
- shapeOption,
231
- shapeSizeOption,
232
- {
233
- type: "term",
234
- configKey: "scaleDotTW",
235
- chartType: "runChart",
236
- usecase: { target: "runChart", detail: "numeric" },
237
- title: "Scale sample by term value",
238
- label: "Scale by",
239
- vocabApi: this.runchart.app.vocabApi,
240
- numericEditMenuVersion: ["continuous"]
241
- },
242
- {
243
- label: "Opacity",
244
- type: "number",
245
- chartType: "runChart",
246
- settingsKey: "opacity",
247
- title: "It represents the opacity of the elements",
248
- min: 0,
249
- max: 1,
250
- step: 0.1
251
- },
252
- {
253
- label: "Chart width",
254
- type: "number",
255
- chartType: "runChart",
256
- settingsKey: "svgw"
257
- },
258
- {
259
- label: "Chart height",
260
- type: "number",
261
- chartType: "runChart",
262
- settingsKey: "svgh"
263
- },
264
- {
265
- label: "Default color",
266
- type: "color",
267
- chartType: "runChart",
268
- settingsKey: "defaultColor"
269
- },
270
- {
271
- label: "Save zoom transform",
272
- boxLabel: "",
273
- type: "checkbox",
274
- chartType: "runChart",
275
- settingsKey: "saveZoomTransform",
276
- title: `Option to save the zoom transformation in the state. Needed if you want to save a session with zoom and pan applied`,
277
- processInput: (value) => this.saveZoomTransform(value)
278
- },
279
- {
280
- label: "Exclude outliers",
281
- boxLabel: "",
282
- type: "checkbox",
283
- chartType: "runChart",
284
- settingsKey: "excludeOutliers",
285
- title: `Option to exclude outliers from the analysis`
286
- }
287
- ]
288
- );
289
- if (this.runchart.config.scaleDotTW)
290
- inputs.splice(inputs.length - 5, 0, minShapeSizeOption, maxShapeSizeOption, {
291
- label: "Scale order",
292
- type: "radio",
293
- chartType: "runChart",
294
- settingsKey: "scaleDotOrder",
295
- options: [
296
- { label: "Ascending", value: "Ascending" },
297
- { label: "Descending", value: "Descending" }
298
- ]
299
- });
300
- if (!this.runchart.config.term0)
301
- inputs.push({
302
- label: "Show regression",
303
- type: "dropdown",
304
- chartType: "runChart",
305
- settingsKey: "regression",
306
- options: [
307
- { label: "None", value: "None" },
308
- //{ label: 'Loess', value: 'Loess' },
309
- { label: "Lowess", value: "Lowess" },
310
- { label: "Polynomial", value: "Polynomial" }
311
- ]
312
- });
313
- inputs.push(...this.getMinMaxInputs());
314
- return inputs;
315
- }
316
- };
317
-
318
- // plots/runchart/runchart.ts
319
- var Runchart = class _Runchart extends Scatter {
320
- static {
321
- this.type = "runChart";
322
- }
323
- constructor(opts, api) {
324
- super(opts, api);
325
- this.type = _Runchart.type;
326
- }
327
- async init(appState) {
328
- const state = this.getState(appState);
329
- this.config = structuredClone(state.config);
330
- this.view = new RunchartView(this);
331
- this.model = new RunchartModel(this);
332
- this.vm = new RunchartViewModel(this);
333
- this.interactivity = new ScatterInteractivity(this);
334
- }
335
- async main() {
336
- this.config = structuredClone(this.state.config);
337
- this.settings = this.config.settings[this.type];
338
- await this.model.initData();
339
- await this.model.processData();
340
- this.cat2Color = getColors(this.model.charts.length);
341
- await this.setControls();
342
- this.vm.render();
343
- this.view.dom.loadingDiv.style("display", "none");
344
- this.vm.setTools();
345
- }
346
- async setControls() {
347
- this.view.dom.controlsHolder.selectAll("*").remove();
348
- const inputs = await this.view.getControlInputs();
349
- this.components = {
350
- controls: await controlsInit({
351
- app: this.app,
352
- id: this.id,
353
- holder: this.view.dom.controlsHolder,
354
- inputs
355
- })
356
- };
357
- this.components.controls.on("downloadClick.scatter", (event) => {
358
- this.download(event);
359
- });
360
- }
361
- };
362
- async function getPlotConfig(opts, app) {
363
- const defaultConfig = app.vocabApi.termdbConfig?.plotConfigByCohort?.default?.[opts.chartType];
364
- const settings = copyMerge(getDefaultRunChartSettings(), defaultConfig?.settings);
365
- const plot = {
366
- settings: {
367
- controls: {
368
- isOpen: false
369
- // control panel is hidden by default
370
- },
371
- runChart: settings,
372
- startColor: {},
373
- //dict to store the start color of the gradient for each chart when using continuous color
374
- stopColor: {}
375
- //dict to store the stop color of the gradient for each chart when using continuous color
376
- }
377
- };
378
- opts.filter = app.vocabApi?.termdbConfig?.authFilter;
379
- copyMerge(plot, defaultConfig, opts);
380
- try {
381
- if (plot.colorTW) await fillTermWrapper(plot.colorTW, app.vocabApi);
382
- if (plot.shapeTW) await fillTermWrapper(plot.shapeTW, app.vocabApi);
383
- if (!plot.term.q) plot.term.q = {};
384
- if (!plot.term2.q) plot.term2.q = {};
385
- plot.term.q.mode = "continuous";
386
- plot.term2.q.mode = "continuous";
387
- await fillTermWrapper(plot.term, app.vocabApi);
388
- await fillTermWrapper(plot.term2, app.vocabApi);
389
- if (plot.term0) await fillTermWrapper(plot.term0, app.vocabApi);
390
- if (plot.scaleDotTW) await fillTermWrapper(plot.scaleDotTW, app.vocabApi);
391
- return plot;
392
- } catch (e) {
393
- console.log(e);
394
- throw `${e} [runChart getPlotConfig()]`;
395
- }
396
- }
397
- var runChartInit = getCompInit(Runchart);
398
- var componentInit = runChartInit;
399
- function makeChartBtnMenu(holder, chartsInstance) {
400
- const menuDiv = holder.append("div");
401
- menuDiv.append("button").style("margin", "5px").style("padding", "10px 15px").style("border-radius", "20px").style("border-color", "#ededed").style("display", "block").text("Select data to plot ...").on("click", () => {
402
- chartsInstance.dom.tip.clear();
403
- select2Terms(chartsInstance.dom.tip, chartsInstance.app, "runChart", "date", callback, "numeric");
404
- chartsInstance.dom.tip.show();
405
- });
406
- for (const plot of chartsInstance.state.termdbConfig?.plotConfigByCohort?.default?.runChart?.plots || []) {
407
- const config = structuredClone(plot);
408
- menuDiv.append("button").style("margin", "5px").style("padding", "10px 15px").style("border-radius", "20px").style("border-color", "#ededed").style("display", "block").text(plot.name).on("click", () => {
409
- chartsInstance.app.dispatch({
410
- type: "plot_create",
411
- config: {
412
- chartType: "runChart",
413
- ...config
414
- }
415
- });
416
- chartsInstance.dom.tip.hide();
417
- });
418
- }
419
- const callback = (xterm, yterm) => {
420
- chartsInstance.app.dispatch({
421
- type: "plot_create",
422
- config: {
423
- chartType: "runChart",
424
- term: { term: xterm, q: { mode: "continuous" } },
425
- term2: { term: yterm, q: { mode: "continuous" } },
426
- name: `${xterm.name} vs ${yterm.name}`
427
- }
428
- });
429
- };
430
- }
431
- function getDefaultRunChartSettings() {
432
- return {
433
- aggregateData: "None",
434
- size: 0.5,
435
- minShapeSize: 0.5,
436
- maxShapeSize: 4,
437
- scaleDotOrder: "Ascending",
438
- refSize: 0.8,
439
- svgw: 1e3,
440
- svgh: 500,
441
- axisTitleFontSize: 16,
442
- opacity: 0.6,
443
- defaultColor: plotColor,
444
- regression: "None",
445
- // Color scale configuration settings
446
- // These settings control how numerical values are mapped to colors
447
- colorScaleMode: "auto",
448
- // Default to automatic scaling based on data range
449
- // Other options: 'fixed' (user-defined range) or
450
- // 'percentile' (scale based on data distribution)
451
- colorScalePercentile: 95,
452
- // Default percentile for percentile mode
453
- // This means we'll scale colors based on values
454
- // up to the 95th percentile by default
455
- colorScaleMinFixed: null,
456
- // User-defined minimum value for fixed mode
457
- // Null indicates this hasn't been set yet
458
- colorScaleMaxFixed: null,
459
- // User-defined maximum value for fixed mode
460
- saveZoomTransform: false,
461
- excludeOutliers: false,
462
- minXScale: null,
463
- maxXScale: null,
464
- minYScale: null,
465
- maxYScale: null
466
- };
467
- }
468
-
469
- export {
470
- RunchartModel,
471
- RunchartViewModel,
472
- RunchartView,
473
- Runchart,
474
- getPlotConfig,
475
- runChartInit,
476
- componentInit,
477
- makeChartBtnMenu,
478
- getDefaultRunChartSettings
479
- };
480
- //# sourceMappingURL=chunk-7LKSKJCV.js.map
@@ -1,190 +0,0 @@
1
- import {
2
- sample_match_termvaluesetting
3
- } from "./chunk-UT6W4ZZL.js";
4
- import {
5
- isDictionaryType
6
- } from "./chunk-RYRCMHYR.js";
7
- import {
8
- __export
9
- } from "./chunk-HFNDKYVF.js";
10
-
11
- // plots/matrix/matrix.data.js
12
- var matrix_data_exports = {};
13
- __export(matrix_data_exports, {
14
- applyLegendValueFilter: () => applyLegendValueFilter,
15
- getMatrixRequestOpts: () => getMatrixRequestOpts,
16
- mayRequireToken: () => mayRequireToken,
17
- setData: () => setData
18
- });
19
- function mayRequireToken(tokenMessage = "") {
20
- const message = tokenMessage || this.state.tokenVerificationMessage;
21
- if (!message && this.state.hasVerifiedToken) {
22
- this.dom.errdiv.style("display", "none").html();
23
- this.dom.controls.style("display", this.opts.controls ? "inline-block" : "");
24
- this.dom.svg.style("display", "");
25
- return false;
26
- } else {
27
- this.dom.errdiv.style("display", "").html(message || "Requires login");
28
- this.dom.controls.style("display", "none");
29
- this.dom.svg.style("display", "none");
30
- return true;
31
- }
32
- }
33
- function getMatrixRequestOpts(state) {
34
- const terms = [];
35
- const termgroups = this.chartType == "hierCluster" ? state.config.termgroups.filter((grp) => grp.type != "hierCluster") : state.config.termgroups;
36
- for (const grp of termgroups) {
37
- terms.push(...getNormalizedTwLstCopy(grp.lst));
38
- }
39
- if (state.config.divideBy) terms.push(normalizeTwForRequest(structuredClone(state.config.divideBy)));
40
- const opts = {
41
- terms,
42
- filter: state.filter,
43
- filter0: state.filter0,
44
- maxGenes: state.config.settings.matrix.maxGenes,
45
- /*********** quick fix
46
- when the flag is true, set artificially large number to ensure all genes are sent in one query
47
- this avoids changing getAnnotatedSampleData()
48
- additional non-matrix app that calls getAnnotatedSampleData will NEED THE SAME FIX
49
- */
50
- termsPerRequest: this.app.vocabApi.termdbConfig.queries?.snvindel?.byisoform?.processTwsInOneQuery ? 1e3 : 1
51
- };
52
- if (this.chartType == "hierCluster") {
53
- opts.isHierCluster = 1;
54
- }
55
- return opts;
56
- }
57
- function getNormalizedTwLstCopy(twlst) {
58
- const lst = structuredClone(twlst);
59
- lst.forEach(normalizeTwForRequest);
60
- lst.sort(sortTwLst);
61
- return lst;
62
- }
63
- function normalizeTwForRequest(tw) {
64
- if (!tw?.term) return;
65
- delete tw.term.category2samplecount;
66
- if (isDictionaryType(tw.term.type) && tw.term.type !== "samplelst") delete tw.term.values;
67
- return tw;
68
- }
69
- function sortTwLst(twa, twb) {
70
- const a = twa?.$id || twa.term?.id || twa?.term?.name;
71
- const b = twb?.$id || twb.term?.id || twb?.term?.name;
72
- return a < b ? -1 : 1;
73
- }
74
- async function setData(_data) {
75
- const opts = this.currRequestOpts?.matrix || this.getMatrixRequestOpts(this.state);
76
- this.numTerms = opts.terms.length;
77
- const abortCtrl = new AbortController();
78
- opts.signal = abortCtrl.signal;
79
- opts.loadingDiv = this.chartType != "hierCluster" && this.dom.loadingDiv;
80
- const data = await this.app.vocabApi.getAnnotatedSampleData(opts, _data);
81
- this.data = data;
82
- this.origData = structuredClone(this.data);
83
- this.sampleIdMap = {};
84
- for (const d of this.data.lst) {
85
- this.sampleIdMap[d.sample] = d._ref_.label;
86
- }
87
- }
88
- function applyLegendValueFilter() {
89
- const self = this;
90
- if (!self.config.legendValueFilter.lst.length && !self.config.legendGrpFilter.lst.length) return;
91
- for (const grpFilter of self.config.legendGrpFilter.lst) {
92
- if (grpFilter.dt) {
93
- const filteredOutCats = /* @__PURE__ */ new Set();
94
- for (const oneSampleData of self.origData.lst) {
95
- for (const annoForOneTerm of Object.values(oneSampleData)) {
96
- if (annoForOneTerm.values) {
97
- const newValues = [];
98
- for (const v of annoForOneTerm.values) {
99
- if (!(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))) {
100
- newValues.push(v);
101
- } else {
102
- filteredOutCats.add(v.class);
103
- }
104
- }
105
- annoForOneTerm.values = newValues;
106
- }
107
- }
108
- }
109
- grpFilter.filteredOutCats = [...filteredOutCats];
110
- for (const oneSampleData of Object.values(self.origData.samples)) {
111
- for (const annoForOneTerm of Object.values(oneSampleData)) {
112
- if (annoForOneTerm.values)
113
- annoForOneTerm.values = annoForOneTerm.values.filter(
114
- (v) => !(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))
115
- );
116
- }
117
- }
118
- }
119
- }
120
- const geneVariant$ids = Object.values(self.data.refs.byTermId).filter((v) => v.term?.type == "geneVariant").map((v) => v.$id);
121
- const data = { samples: {}, lst: [], refs: self.data.refs };
122
- const onlyHardFilter = structuredClone(self.config.legendValueFilter);
123
- onlyHardFilter.lst = onlyHardFilter.lst.filter(
124
- (l) => !l.tvs.legendFilterType || l.tvs.legendFilterType !== "geneVariant_soft"
125
- );
126
- for (const row of self.origData.lst) {
127
- const include = sample_match_termvaluesetting(row, onlyHardFilter, geneVariant$ids);
128
- if (include || self.chartType == "hierCluster") {
129
- data.samples[row.sample] = row;
130
- data.lst.push(row);
131
- }
132
- }
133
- for (const valFilter of self.config.legendValueFilter.lst) {
134
- if (valFilter.tvs.legendFilterType !== "geneVariant_soft") continue;
135
- const tvsV = valFilter.tvs.values[0];
136
- const filteredOutCats = /* @__PURE__ */ new Set();
137
- for (const oneSampleData of data.lst) {
138
- for (const annoForOneTerm of Object.values(oneSampleData)) {
139
- if (annoForOneTerm.values) {
140
- const newValues = [];
141
- for (const v of annoForOneTerm.values) {
142
- if (!(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))) {
143
- newValues.push(v);
144
- } else {
145
- filteredOutCats.add(v.class);
146
- }
147
- }
148
- annoForOneTerm.values = newValues;
149
- }
150
- }
151
- }
152
- valFilter.filteredOutCats = [...filteredOutCats];
153
- for (const oneSampleData of Object.values(data.samples)) {
154
- for (const annoForOneTerm of Object.values(oneSampleData)) {
155
- if (annoForOneTerm.values)
156
- annoForOneTerm.values = annoForOneTerm.values.filter(
157
- (v) => !(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))
158
- );
159
- }
160
- }
161
- }
162
- if (self.chartType !== "hierCluster" && geneVariant$ids.length && self.app.vocabApi.vocab?.dslabel == "GDC")
163
- remove_empty_sample(data, geneVariant$ids);
164
- self.data = data;
165
- }
166
- function remove_empty_sample(data) {
167
- for (const oneSampleData of data.lst) {
168
- let removeSample = true;
169
- for (const [key, annoForOneTerm] of Object.entries(oneSampleData)) {
170
- if (!annoForOneTerm.values) continue;
171
- const annoType = data.refs.byTermId[key].term.type;
172
- if (annoType != "geneVariant") continue;
173
- if (annoForOneTerm.values.length) removeSample = false;
174
- }
175
- if (removeSample) {
176
- data.lst = data.lst.filter((dl) => dl.sample !== oneSampleData.sample);
177
- delete data.samples[parseInt(oneSampleData.sample)];
178
- }
179
- }
180
- return data;
181
- }
182
-
183
- export {
184
- mayRequireToken,
185
- getMatrixRequestOpts,
186
- setData,
187
- applyLegendValueFilter,
188
- matrix_data_exports
189
- };
190
- //# sourceMappingURL=chunk-7P67W6NF.js.map