@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

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 (848) hide show
  1. package/dist/2dmaf-F5QNP7AQ.js +1371 -0
  2. package/dist/AIProjectAdmin-ROSQHK6Q.js +827 -0
  3. package/dist/AIProjectAdmin-ROSQHK6Q.js.map +7 -0
  4. package/dist/AppHeader-STVCDLET.js +833 -0
  5. package/dist/BoxPlot-CU7MEBH7.js +1217 -0
  6. package/dist/CorrelationVolcano-OE4R2GS3.js +617 -0
  7. package/dist/DE-SR7PJPKI.js +93 -0
  8. package/dist/DEinput-PRIAIBFH.js +299 -0
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  10. package/dist/DifferentialAnalysis-UWTYK7NU.js +241 -0
  11. package/dist/Disco-IL6REGSA.js +3235 -0
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  154. package/dist/dictionary-BSKN37CP.js +109 -0
  155. package/dist/dnaMethylation-5QNEEGC6.js +36 -0
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  165. package/dist/geneExpression-NAM2UEYN.js +36 -0
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  806. /package/dist/{singlecell-VJJZJZF7.js.map → singlecell-FK5JETW5.js.map} +0 -0
  807. /package/dist/{singlecell-VQJ2252L.js.map → singlecell-RL7V7DIC.js.map} +0 -0
  808. /package/dist/{snp-ALMKZKL2.js.map → snp-FT7HB3XN.js.map} +0 -0
  809. /package/dist/{snp.unit.spec-GJQBAHGQ.js.map → snp.unit.spec-CLYVYPPG.js.map} +0 -0
  810. /package/dist/{snplocus-WCNCMFWZ.js.map → snplocus-M5SEQGAC.js.map} +0 -0
  811. /package/dist/{spliceevent.a53ss.diagram-4Q4JF4RX.js.map → spliceevent.a53ss.diagram-EJ5CTRCZ.js.map} +0 -0
  812. /package/dist/{spliceevent.exonskip.diagram-IOYOKELT.js.map → spliceevent.exonskip.diagram-ETXMOHZ3.js.map} +0 -0
  813. /package/dist/{spliceevent.noeventdiagram-77ZCOHSF.js.map → spliceevent.noeventdiagram-S2O4ZM2Z.js.map} +0 -0
  814. /package/dist/{ssGSEA-QTXXIN4K.js.map → ssGSEA-6PMDQDTJ.js.map} +0 -0
  815. /package/dist/{ssGSEA.unit.spec-LQESATT3.js.map → ssGSEA.unit.spec-JD5T4R2N.js.map} +0 -0
  816. /package/dist/{summarizeCnvGeneexp-YKUQGDQF.js.map → summarizeCnvGeneexp-GCHNKTIU.js.map} +0 -0
  817. /package/dist/{summarizeGeneexpSurvival-ARGG5VDC.js.map → summarizeGeneexpSurvival-R2RYQZ3M.js.map} +0 -0
  818. /package/dist/{summarizeMutationCnv-FMZYT3EC.js.map → summarizeMutationCnv-LB2BIYRL.js.map} +0 -0
  819. /package/dist/{summarizeMutationDiagnosis-ZX7I46SC.js.map → summarizeMutationDiagnosis-3JUY75LM.js.map} +0 -0
  820. /package/dist/{summarizeMutationSurvival-RCFMTT43.js.map → summarizeMutationSurvival-VYLRWTCF.js.map} +0 -0
  821. /package/dist/{summary-QLL5YVI2.js.map → summary-2QQ72IEQ.js.map} +0 -0
  822. /package/dist/{summary.integration.spec-DHY6XCEJ.js.map → summary.integration.spec-XXU362UQ.js.map} +0 -0
  823. /package/dist/{summaryInput-ANCUQGIB.js.map → summaryInput-OZHZG3PV.js.map} +0 -0
  824. /package/dist/{sunburst-RDNFBOCK.js.map → sunburst-CMCJCANX.js.map} +0 -0
  825. /package/dist/{survival-BG7QV52L.js.map → survival-EBD4DHO7.js.map} +0 -0
  826. /package/dist/{survival-WSN36OQE.js.map → survival-ISLRRPKU.js.map} +0 -0
  827. /package/dist/{survival.integration.spec-37KAJ5IK.js.map → survival.integration.spec-FS7V4OXK.js.map} +0 -0
  828. /package/dist/{svgraph-A5WGHW4S.js.map → svgraph-KGLNUM7W.js.map} +0 -0
  829. /package/dist/{svmr-CYRHHWZF.js.map → svmr-NXZ5VLKH.js.map} +0 -0
  830. /package/dist/{table-VHO7E5PI.js.map → table-ISOQOI6C.js.map} +0 -0
  831. /package/dist/{termCollection-HSVSH7TJ.js.map → termCollection-7ZSU3I45.js.map} +0 -0
  832. /package/dist/{termCollection-E4Q6GLXN.js.map → termCollection-V2A5BDQB.js.map} +0 -0
  833. /package/dist/{termCollection.unit.spec-ZCE3TUMS.js.map → termCollection.unit.spec-6VLCJGOU.js.map} +0 -0
  834. /package/dist/{tk-GPRHDN4K.js.map → tk-6AB6XYIE.js.map} +0 -0
  835. /package/dist/{tp.ui-LTUA3FSL.js.map → tp.ui-2O4UW5N7.js.map} +0 -0
  836. /package/dist/{tvs.dt-G43PAAKD.js.map → tvs.dt-CY6TOQVB.js.map} +0 -0
  837. /package/dist/{tvs.dtcnv.categorical-UHDS2TGZ.js.map → tvs.dtcnv.categorical-AYQ432TW.js.map} +0 -0
  838. /package/dist/{tvs.dtcnv.continuous-ZNGYQKTD.js.map → tvs.dtcnv.continuous-XVDL6SG3.js.map} +0 -0
  839. /package/dist/{tvs.dtfusion-JBEEUDUS.js.map → tvs.dtfusion-V3AV7A6Q.js.map} +0 -0
  840. /package/dist/{tvs.dtsnvindel-XXN5Q7RN.js.map → tvs.dtsnvindel-XM3NXIT7.js.map} +0 -0
  841. /package/dist/{tvs.dtsv-MO6L7HHV.js.map → tvs.dtsv-Z2GYRINW.js.map} +0 -0
  842. /package/dist/{tvs.samplelst-HKY6UUJM.js.map → tvs.samplelst-C4FB63G7.js.map} +0 -0
  843. /package/dist/{tvs.termCollection-TY6FPL25.js.map → tvs.termCollection-VHTSC2ST.js.map} +0 -0
  844. /package/dist/{violin-YHE3WSGR.js.map → violin-KGGTUQFF.js.map} +0 -0
  845. /package/dist/{violin.integration.spec-F2UD7BHC.js.map → violin.integration.spec-5EW6PLJX.js.map} +0 -0
  846. /package/dist/{violin.interactivity-LVDTDEPQ.js.map → violin.interactivity-RI4RURGO.js.map} +0 -0
  847. /package/dist/{violin.renderer-IIEIUGRI.js.map → violin.renderer-EWU2IFZE.js.map} +0 -0
  848. /package/dist/{vocabulary-WQRYXBRO.js.map → vocabulary-VLIGC7OP.js.map} +0 -0
@@ -1,56 +0,0 @@
1
- import {
2
- sayerror
3
- } from "./chunk-YWUVCXFS.js";
4
- import {
5
- TermTypeGroups
6
- } from "./chunk-AMYSEKPF.js";
7
-
8
- // termdb/handlers/singleCellCellType.ts
9
- var SearchHandler = class {
10
- async init(opts) {
11
- this.validateOpts(opts);
12
- this.callback = opts.callback;
13
- this.app = opts.app;
14
- const holder = opts.holder.append("div").style("padding", "10px 0px");
15
- const scctTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE];
16
- if (!scctTerms) {
17
- sayerror(
18
- holder,
19
- `termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`
20
- );
21
- return;
22
- }
23
- const usecaseConfig = opts.usecase?.specialCase?.config;
24
- const plotName = usecaseConfig?.name;
25
- let filteredTerms = [];
26
- if (plotName) {
27
- filteredTerms = scctTerms.filter((t) => t.plot == plotName);
28
- } else {
29
- filteredTerms = scctTerms.map((t) => Object.assign(t, { label: `${t.name} (${t.plot})` }));
30
- }
31
- for (const t of filteredTerms) {
32
- holder.append("div").classed("termdiv", true).style("padding", "0px 5px").append("div").classed("termlabel sja_filter_tag_btn sja_tree_click_term ts_pill", true).style("display", "inline-block").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text(t.label || t.name).on("click", () => {
33
- const term = this.makeTerm(t, usecaseConfig);
34
- this.callback(term);
35
- });
36
- }
37
- }
38
- makeTerm(_term, usecaseConfig) {
39
- const term = { ..._term };
40
- if (!term.sample && usecaseConfig?.sample) term.sample = usecaseConfig.sample;
41
- return term;
42
- }
43
- validateOpts(opts) {
44
- if (opts.callback == null) throw new Error("callback is required");
45
- if (opts.app == null) throw new Error("app is required");
46
- if (opts.holder == null) throw new Error("holder is required");
47
- if (opts.usecase == null) throw new Error("usecase is required");
48
- if (!opts.app.vocabApi.termdbConfig?.termType2terms)
49
- throw new Error("termType2terms is required in termdbConfig for singleCellCellType handler");
50
- }
51
- };
52
-
53
- export {
54
- SearchHandler
55
- };
56
- //# sourceMappingURL=chunk-PZ3KIUWJ.js.map
@@ -1,335 +0,0 @@
1
- import {
2
- storeInit
3
- } from "./chunk-JMJW3ERE.js";
4
- import {
5
- summaryInit
6
- } from "./chunk-3T2PCWII.js";
7
- import {
8
- navInit
9
- } from "./chunk-ZT3PB4XX.js";
10
- import {
11
- AppBase,
12
- downloadSVGsAsPdf,
13
- filterRxCompInit,
14
- newSandboxDiv,
15
- sayerror,
16
- vocabInit
17
- } from "./chunk-YWUVCXFS.js";
18
- import {
19
- importPlot
20
- } from "./chunk-3QBZ2Y77.js";
21
- import {
22
- Menu
23
- } from "./chunk-HYOEWQ5P.js";
24
- import {
25
- AppApi,
26
- getCompInit,
27
- multiInit
28
- } from "./chunk-MVTCBVSX.js";
29
- import {
30
- select_default
31
- } from "./chunk-I6Y4O3RR.js";
32
-
33
- // mass/plot.js
34
- var MassPlot = class _MassPlot {
35
- static type = "plot";
36
- constructor(opts) {
37
- this.type = _MassPlot.type;
38
- setRenderers(this);
39
- this.initUi(opts);
40
- }
41
- reactsTo(action) {
42
- if (action.type.includes("cache_termq")) return true;
43
- if (action.type.endsWith("_group")) return true;
44
- if (action.type.startsWith("plot_")) {
45
- return action.id === this.id || action.id == this.parentId || action.config?.parentId === this.id || action.parentId === this.id;
46
- }
47
- if (action.type.startsWith("filter")) return true;
48
- if (action.type.startsWith("cohort")) return true;
49
- if (action.type == "app_refresh") return true;
50
- if (action.type.endsWith("customTerm")) return true;
51
- }
52
- // !!! NOTE: This getState() method is reused by the plot-specific recover component.
53
- // When logging something within getState, it may have been called by either the plot or recover instance
54
- getState(appState) {
55
- const config = appState.plots.find((p) => p.id === this.id);
56
- if (!config) {
57
- throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
58
- }
59
- return {
60
- termfilter: appState.termfilter,
61
- config,
62
- groups: appState.groups,
63
- // quick fix to skip history tracking as needed
64
- _scope_: appState._scope_
65
- };
66
- }
67
- async main() {
68
- this.dom.errdiv.style("display", "none").style("background-color", "rgba(255,100,100,0.2)").html("");
69
- if (!this.components) await this.setComponents(this.opts);
70
- }
71
- async setComponents(opts) {
72
- const _ = await importPlot(opts.chartType);
73
- const promises = {
74
- // recover: recoverInit({
75
- // app: this.app,
76
- // holder: this.dom.localRecoverDiv,
77
- // getState: appState => this.getState(appState),
78
- // reactsTo: action =>
79
- // action.id == this.id &&
80
- // (action.type == 'plot_edit' || action.type == 'plot_nestedEdits') &&
81
- // action._track_ != 'none',
82
- // plot_id: this.id,
83
- // maxHistoryLen: 10,
84
- // hideLabel: true
85
- // }),
86
- chart: _.componentInit({
87
- app: this.app,
88
- holder: this.dom.viz,
89
- header: this.dom.paneTitleDiv,
90
- id: this.id,
91
- plotDiv: select_default(this.dom.holder.app_div.node().parentNode),
92
- /******* reason for passing plotDiv to chart ********
93
- - this plot instance may allow to launch a new plot as a persistent sandbox
94
- inside mass plotDiv, maintaining the uniform plot appearance despite it's ad-hoc
95
- the new plot is not a formal mass plot type, and cannot be done via app.dispatch()
96
- thus the need to directly access plotDiv
97
- - example: mds3 tk from genome browser can launch disco etc
98
- - having access to plotDiv may offer flexibility for the plot to do stuff
99
-
100
- since plot.js has no access to mass app .dom.plotDiv in which all apps are shown,
101
- this workarounds gets the parent node of sandbox.app_div which is app.dom.plotDiv
102
- */
103
- getFilterImage: async () => this.components.filter.getFilterImage()
104
- })
105
- };
106
- if (!this.state.config.hidePlotFilter)
107
- promises.filter = filterRxCompInit({
108
- app: this.app,
109
- vocabApi: this.app.vocabApi,
110
- parentId: this.id,
111
- holder: this.dom.filterDiv,
112
- hideLabel: true,
113
- emptyLabel: "+Add new filter",
114
- callback: (filter) => {
115
- this.app.dispatch({
116
- id: this.id,
117
- type: "plot_edit",
118
- config: { filter }
119
- });
120
- }
121
- });
122
- this.components = await multiInit(promises);
123
- }
124
- destroy() {
125
- this.dom.holder.app_div.selectAll("*").remove();
126
- this.dom.holder.app_div.remove();
127
- for (const key in this.dom) {
128
- delete this.dom[key];
129
- }
130
- }
131
- };
132
- var plotInit = getCompInit(MassPlot);
133
- function setRenderers(self) {
134
- self.initUi = function(opts) {
135
- const holder = opts.holder;
136
- opts.holder.app_div.attr("data-testid", "sjpp-massplot-sandbox-" + opts.chartType);
137
- holder.header.style("padding", 0);
138
- try {
139
- self.dom = {
140
- tip: new Menu({ padding: "0px" }),
141
- holder,
142
- paneTitleDiv: holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px").style("vertical-align", "sub"),
143
- localRecoverDiv: holder.header.append("div").style("display", "inline-block"),
144
- filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9),
145
- body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
146
- // will hold no data notice or the page title in multichart views
147
- errdiv: holder.body.append("div").style("display", "none").style("padding", "5px").style("background-color", "rgba(255,100,100,0.2)"),
148
- // dom.viz will hold the rendered view
149
- viz: holder.body.append("div")
150
- };
151
- } catch (e) {
152
- self.dom.errdiv.style("display", "none").text(e);
153
- }
154
- };
155
- }
156
-
157
- // mass/app.ts
158
- var MassApp = class extends AppBase {
159
- // expected class-specific props
160
- constructor(opts, api) {
161
- super(opts);
162
- this.components = {};
163
- this.wasDestroyed = false;
164
- this.api = api;
165
- if (opts.addLoginCallback) {
166
- opts.addLoginCallback(() => this.api.dispatch({ type: "app_refresh" }));
167
- }
168
- this.type = "app";
169
- this.dom = {
170
- holder: opts.holder,
171
- // do not modify holder style
172
- topbar: opts.holder.append("div"),
173
- errdiv: opts.holder.append("div"),
174
- plotDiv: opts.holder.append("div")
175
- };
176
- this.plotIdToSandboxId = {};
177
- }
178
- static {
179
- this.type = "app";
180
- }
181
- async preApiFreeze(api) {
182
- try {
183
- api.tip = new Menu({ padding: "5px" });
184
- api.tip.d.on("keyup", (event) => {
185
- if (event.key == "Escape") api.tip.hide();
186
- });
187
- api.printError = (e) => this.printError(e);
188
- api.vocabApi = await vocabInit({
189
- app: api,
190
- state: { vocab: this.opts.state.vocab },
191
- fetchOpts: this.opts.fetchOpts,
192
- getDatasetAccessToken: this.opts.getDatasetAccessToken
193
- });
194
- api.hasWebGL = function() {
195
- try {
196
- const canvas = document.createElement("canvas");
197
- return !!(window.WebGLRenderingContext && (canvas.getContext("webgl") || canvas.getContext("experimental-webgl")));
198
- } catch (_) {
199
- return false;
200
- }
201
- };
202
- this.opts.state.vocab = api.vocabApi.vocab;
203
- } catch (e) {
204
- console.log(`preApiFreeze error`, e);
205
- throw e;
206
- }
207
- }
208
- async init() {
209
- try {
210
- const debounceInterval = "debounceInterval" in this.opts ? this.opts.debounceInterval : 0;
211
- const embeddedSessionState = this.opts.embeddedSessionState;
212
- if (embeddedSessionState) {
213
- Object.assign(this.opts.state, embeddedSessionState);
214
- }
215
- this.store = await storeInit({ app: this.api, state: this.opts.state, debounceInterval });
216
- this.state = await this.store.copyState();
217
- this.components = {};
218
- if (this.state.nav.header_mode != "hidden") {
219
- this.components.nav = await navInit({
220
- app: this.api,
221
- holder: this.dom.topbar,
222
- header_mode: this.state && this.state.nav && this.state.nav.header_mode,
223
- vocab: this.state.vocab,
224
- massSessionDuration: this.state.termdbConfig.massSessionDuration,
225
- // this.opts.massSessionDuration
226
- pkgver: this.opts.pkgver,
227
- downloadPlots: () => {
228
- this.downloadPlots();
229
- }
230
- });
231
- }
232
- this.components.plots = {};
233
- if (this.opts.app?.doNotAwaitInitRender) {
234
- this.api.dispatch();
235
- } else {
236
- await this.api.dispatch();
237
- }
238
- } catch (e) {
239
- this.printError(e);
240
- throw e;
241
- }
242
- }
243
- async main() {
244
- await this.api.vocabApi.main();
245
- this.dom.plotDiv?.style(
246
- "display",
247
- this.state.nav?.header_mode != "hidden" && this.state.nav?.activeTab == 0 ? "none" : "block"
248
- );
249
- const newPlots = {};
250
- let sandbox;
251
- for (const plot of this.state.plots) {
252
- if (plot.parentId) continue;
253
- if (this.components.plots && !(plot.id in this.components.plots)) {
254
- sandbox = newSandboxDiv(this.dom.plotDiv, {
255
- close: () => {
256
- this.api.dispatch({
257
- type: "plot_delete",
258
- id: plot.id
259
- });
260
- },
261
- plotId: plot.id,
262
- beforePlotId: plot.insertBefore || null,
263
- style: {
264
- width: "98.5%"
265
- }
266
- });
267
- if (plot.chartType == "summary")
268
- newPlots[plot.id] = summaryInit(Object.assign({ app: this.api, holder: sandbox }, plot));
269
- else newPlots[plot.id] = plotInit(Object.assign({ app: this.api, holder: sandbox }, plot));
270
- }
271
- }
272
- const numNewPlots = Object.keys(newPlots).length;
273
- if (numNewPlots) {
274
- await Promise.all(Object.values(newPlots));
275
- for (const plotId in newPlots) {
276
- this.components.plots[plotId] = await newPlots[plotId];
277
- }
278
- }
279
- for (const plotId in this.components.plots) {
280
- if (!this.state.plots.find((p) => p.id === plotId)) {
281
- this.components.plots[plotId].destroy();
282
- delete this.components.plots[plotId];
283
- }
284
- }
285
- }
286
- printError(e) {
287
- const errdiv = e.errdiv || this.dom.errdiv;
288
- if (errdiv) errdiv.style("display", "").html("").style("background-color", "");
289
- sayerror(errdiv || this.opts.holder, "Error: " + (e.message || e.error || e));
290
- if (e.stack) console.log(e.stack);
291
- this.bus.emit("error");
292
- if (this.opts?.debug) console.trace("Trace from MassApp.printError() call");
293
- }
294
- skipPrevActionAbort(action) {
295
- if (!action) return false;
296
- if (action.type.startsWith("filter")) return false;
297
- if (action.type.startsWith("cohort")) return false;
298
- if (action.type == "app_refresh") {
299
- if (action.subactions) {
300
- return action.subactions.find((a) => a.type.startsWith("filter") || a.type.startsWith("cohort")) ? false : true;
301
- }
302
- }
303
- return true;
304
- }
305
- async downloadPlots() {
306
- const chartImagesAll = [];
307
- let i = 1;
308
- const values = Object.values(this.components.plots);
309
- for (const plot of values) {
310
- const chart = plot.type == "plot" ? plot.getComponents("chart") : plot;
311
- const chartImages = chart.getChartImages ? chart.getChartImages() : null;
312
- if (!chartImages) {
313
- console.log(`The ${chart.type} does not support downloading images yet`);
314
- continue;
315
- }
316
- for (const chartImage of chartImages) {
317
- if (values.length > 1) chartImage.name = `${i}. ${chartImage.name}`;
318
- chartImagesAll.push(chartImage);
319
- }
320
- i++;
321
- }
322
- if (chartImagesAll.length > 0) {
323
- const filters = [];
324
- const globalFilterImg = await this.components.nav.getComponents("filter").getFilterImage();
325
- if (globalFilterImg) filters.push(globalFilterImg);
326
- downloadSVGsAsPdf(chartImagesAll, "plots", "landscape", filters);
327
- } else alert("No chart images available for download");
328
- }
329
- };
330
- var appInit = AppApi.getInitFxn(MassApp);
331
-
332
- export {
333
- appInit
334
- };
335
- //# sourceMappingURL=chunk-QEWMCAJW.js.map
@@ -1,129 +0,0 @@
1
- import {
2
- keyupEnter
3
- } from "./chunk-YWUVCXFS.js";
4
-
5
- // src/block.mds.svcnv.share.js
6
- function rnabamtk_initparam(c) {
7
- if (!c.dna_mintotalreads) c.dna_mintotalreads = 8;
8
- if (!c.rna_mintotalreads) c.rna_mintotalreads = 8;
9
- if (!c.hetsnp_minbaf) c.hetsnp_minbaf = 0.3;
10
- if (!c.hetsnp_maxbaf) c.hetsnp_maxbaf = 0.7;
11
- if (c.rnapileup_q == void 0) c.rnapileup_q = 0;
12
- if (!c.rnapileup_Q) c.rnapileup_Q = 13;
13
- if (!c.binompvaluecutoff) c.binompvaluecutoff = 0.05;
14
- if (!c.clientcolor_snpinuse) c.clientcolor_snpinuse = "blue";
15
- if (!c.clientcolor_markernotinuse) c.clientcolor_markernotinuse = "#bbb";
16
- }
17
- function configPanel_rnabam(tk, block, loadTk) {
18
- const c = tk.checkrnabam;
19
- if (!c) return;
20
- tk.tkconfigtip.d.append("hr");
21
- const d = tk.tkconfigtip.d.append("div").style("margin", "15px 0px");
22
- d.append("div").style("opacity", 0.5).style("font-size", ".9em").text("Finding heterozygous SNPs in DNA");
23
- {
24
- const row = d.append("div").style("margin-top", "5px");
25
- row.append("span").html("DNA minimum total read count ");
26
- row.append("input").attr("type", "number").style("width", "50px").property("value", c.dna_mintotalreads).on("keyup", (event) => {
27
- if (!keyupEnter(event)) return;
28
- let v = Number.parseInt(event.target.value);
29
- if (!v || v <= 0) return;
30
- if (c.dna_mintotalreads == v) {
31
- return;
32
- }
33
- c.dna_mintotalreads = v;
34
- loadTk(tk, block);
35
- });
36
- row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total coverage is below cutoff, it will be skipped.");
37
- }
38
- {
39
- const row = d.append("div").style("margin-top", "5px");
40
- row.append("span").html("Heterozygous SNP BAF range&nbsp;&nbsp;");
41
- row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_minbaf).on("keyup", (event) => {
42
- if (!keyupEnter(event)) return;
43
- let v = Number.parseFloat(event.target.value);
44
- if (!v || v <= 0) return;
45
- if (c.hetsnp_minbaf == v) {
46
- return;
47
- }
48
- c.hetsnp_minbaf = v;
49
- loadTk(tk, block);
50
- });
51
- row.append("span").style("opacity", ".5").style("font-size", ".8em").html("&nbsp;&leq; BAF &leq;&nbsp;");
52
- row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_maxbaf).on("keyup", (event) => {
53
- if (!keyupEnter(event)) return;
54
- let v = Number.parseFloat(event.target.value);
55
- if (!v || v <= 0) return;
56
- if (c.hetsnp_maxbaf == v) {
57
- return;
58
- }
59
- c.hetsnp_maxbaf = v;
60
- loadTk(tk, block);
61
- });
62
- row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's BAF (B-allele fraction) is within this range, it is heterozygous.");
63
- }
64
- d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Counting alleles in RNA-seq BAM file");
65
- {
66
- const row = d.append("div").style("margin-top", "5px");
67
- row.append("span").html("Skip alignments with mapQ smaller than&nbsp;");
68
- row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_q).on("keyup", (event) => {
69
- if (!keyupEnter(event)) return;
70
- let v = Number.parseInt(event.target.value);
71
- if (!v || v < 0) return;
72
- if (c.rnapileup_q == v) {
73
- return;
74
- }
75
- c.rnapileup_q = v;
76
- loadTk(tk, block);
77
- });
78
- }
79
- {
80
- const row = d.append("div").style("margin-top", "5px");
81
- row.append("span").html("Skip bases with baseQ/BAQ smaller than&nbsp;");
82
- row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_Q).on("keyup", (event) => {
83
- if (!keyupEnter(event)) return;
84
- let v = Number.parseInt(event.target.value);
85
- if (!v || v <= 0) return;
86
- if (c.rnapileup_Q == v) {
87
- return;
88
- }
89
- c.rnapileup_Q = v;
90
- loadTk(tk, block);
91
- });
92
- }
93
- d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Binomial test on whether a heterozygous SNP shows allelic bias in RNA");
94
- {
95
- const row = d.append("div").style("margin-top", "5px");
96
- row.append("span").html("P-value cutoff&nbsp;");
97
- row.append("input").attr("type", "number").style("width", "50px").property("value", c.binompvaluecutoff).on("keyup", (event) => {
98
- if (!keyupEnter(event)) return;
99
- let v = Number.parseFloat(event.target.value);
100
- if (!v || v <= 0 || v >= 1) return;
101
- if (c.binompvaluecutoff == v) {
102
- return;
103
- }
104
- c.binompvaluecutoff = v;
105
- loadTk(tk, block);
106
- });
107
- }
108
- {
109
- const row = d.append("div").style("margin-top", "5px");
110
- row.append("span").html("RNA minimum total read count&nbsp;");
111
- row.append("input").attr("type", "number").style("width", "50px").property("value", c.rna_mintotalreads).on("keyup", (event) => {
112
- if (!keyupEnter(event)) return;
113
- let v = Number.parseInt(event.target.value);
114
- if (!v || v <= 0) return;
115
- if (c.rna_mintotalreads == v) {
116
- return;
117
- }
118
- c.rna_mintotalreads = v;
119
- loadTk(tk, block);
120
- });
121
- row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total read count from RNA is below cutoff, it won't do binomial test.");
122
- }
123
- }
124
-
125
- export {
126
- rnabamtk_initparam,
127
- configPanel_rnabam
128
- };
129
- //# sourceMappingURL=chunk-QLWDUZ5K.js.map
@@ -1,95 +0,0 @@
1
- import {
2
- getPlotConfig
3
- } from "./chunk-OYEISJSJ.js";
4
- import {
5
- fillTermWrapper
6
- } from "./chunk-YWUVCXFS.js";
7
- import {
8
- copyMerge
9
- } from "./chunk-MVTCBVSX.js";
10
- import {
11
- TermTypes,
12
- numericTypes
13
- } from "./chunk-EGWVYY7K.js";
14
-
15
- // plots/matrix/hierCluster.config.js
16
- async function getPlotConfig2(opts = {}, app) {
17
- opts.chartType = "hierCluster";
18
- const config = await getPlotConfig(opts, app);
19
- delete config.genes;
20
- config.settings.hierCluster = {
21
- /* type of data used for clustering
22
- exciting todo: (to introduce new dt values)
23
- - gene dependency
24
- - numeric dic term
25
- - non-gene genomic stuff that resolves into numeric quantities (cpg meth)
26
- - metabolite
27
- */
28
- dataType: config.dataType,
29
- // adjust the default group name based on automatically detected term types
30
- // Done in matrix.cells.js: setHierClusterCellProps
31
- // termGroupName: 'Expression',
32
- clusterSamples: true,
33
- clusterRows: true,
34
- clusterMethod: "average",
35
- // complete
36
- distanceMethod: "euclidean",
37
- zScoreCap: 5,
38
- zScoreTransformation: true,
39
- xDendrogramHeight: 100,
40
- yDendrogramHeight: 200,
41
- colorScale: "blueWhiteRed"
42
- };
43
- const overrides = app.vocabApi.termdbConfig.hierCluster || {};
44
- const hierClusterSubTypeOverrides = app.vocabApi.termdbConfig[`${config.dataType}Cluster`] || {};
45
- copyMerge(
46
- config.settings.hierCluster,
47
- overrides.settings,
48
- opts.settings?.hierCluster || {},
49
- hierClusterSubTypeOverrides.settings
50
- );
51
- {
52
- const c = config.settings.hierCluster.colorScale;
53
- if (!c) throw "colorScale missing";
54
- }
55
- config.settings.matrix.collabelpos = "top";
56
- const termGroupName = config.settings.hierCluster.termGroupName;
57
- const hcTermGroup = config.termgroups.find((g) => g.type == "hierCluster" || g.name == termGroupName) || {
58
- name: termGroupName
59
- };
60
- hcTermGroup.type = "hierCluster";
61
- if (!hcTermGroup.lst?.length) {
62
- if (!Array.isArray(opts.terms)) throw "opts.terms[] not array (may show geneset edit ui)";
63
- const promises = [];
64
- for (const i of opts.terms) {
65
- const tw = i.term ? i : { term: i };
66
- if (!tw.term.type) {
67
- if (config.dataType == TermTypes.GENE_EXPRESSION || config.dataType == TermTypes.METABOLITE_INTENSITY || config.dataType == TermTypes.PROTEOME_ABUNDANCE) {
68
- tw.term.type = config.dataType;
69
- } else {
70
- throw `term type missing and cannot be assigned by dataType`;
71
- }
72
- } else if (!numericTypes.has(tw.term.type)) {
73
- throw "term type is not numeric";
74
- } else if (config.dataType && !canTermBeInHierGrp(config.dataType, tw.term.type)) {
75
- throw `cannot have term type ${tw.term.type} in ${config.dataType} term group`;
76
- }
77
- promises.push(fillTermWrapper(tw, app.vocabApi));
78
- }
79
- hcTermGroup.lst = await Promise.all(promises);
80
- if (config.termgroups.indexOf(hcTermGroup) == -1) config.termgroups.unshift(hcTermGroup);
81
- }
82
- config.settings.matrix.maxSample = 1e5;
83
- return config;
84
- }
85
- function canTermBeInHierGrp(grpType, twType) {
86
- if (grpType == "numericDictTerm") {
87
- if (twType == "float" || twType == "integer") return true;
88
- }
89
- return twType == grpType;
90
- }
91
-
92
- export {
93
- getPlotConfig2 as getPlotConfig
94
- };
95
- //# sourceMappingURL=chunk-QRSIID3T.js.map