@sjcrh/proteinpaint-client 2.180.0 → 2.180.1

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 (927) hide show
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  2. package/dist/AIProjectAdmin-SAYM2UUO.js +830 -0
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  840. /package/dist/{mds.fimo-TM7YLN4F.js.map → mds.fimo-JWUDO2YS.js.map} +0 -0
  841. /package/dist/{mds.samplescatterplot-LSNRX5LC.js.map → mds.samplescatterplot-H5ZHOO3F.js.map} +0 -0
  842. /package/dist/{mds.survivalplot-PKEVTEC3.js.map → mds.survivalplot-6LJPCDUC.js.map} +0 -0
  843. /package/dist/{oncomatrix-VA5BGIMU.js.map → oncomatrix-5TAYUFN7.js.map} +0 -0
  844. /package/dist/{oncomatrix.spec-ZKSSTD3F.js.map → oncomatrix.spec-4J6ZQSCA.js.map} +0 -0
  845. /package/dist/{plot.2dvaf-PRDECBWZ.js.map → plot.2dvaf-NEKUHMQA.js.map} +0 -0
  846. /package/dist/{plot.app-LMUCBS2S.js.map → plot.app-CDA4NVBW.js.map} +0 -0
  847. /package/dist/{plot.barplot-NI46LKJN.js.map → plot.barplot-WPNGNPFU.js.map} +0 -0
  848. /package/dist/{plot.boxplot-RNJK3TH5.js.map → plot.boxplot-FBHMTSOE.js.map} +0 -0
  849. /package/dist/{plot.brainImaging-5PQKFCME.js.map → plot.brainImaging-53CS65FP.js.map} +0 -0
  850. /package/dist/{plot.disco-NB6EWBO7.js.map → plot.disco-477IKREB.js.map} +0 -0
  851. /package/dist/{plot.dzi-PGWTT7LB.js.map → plot.dzi-37H4EUKF.js.map} +0 -0
  852. /package/dist/{plot.ssgq-XLIV4C3J.js.map → plot.ssgq-WR3HFXR4.js.map} +0 -0
  853. /package/dist/{plot.vaf2cov-QRDE7BXH.js.map → plot.vaf2cov-FCGREDI7.js.map} +0 -0
  854. /package/dist/{plot.wsi-KLYQYZUC.js.map → plot.wsi-HO3DYKJ6.js.map} +0 -0
  855. /package/dist/{polar-LXW6OMOZ.js.map → polar-LRVTYG4P.js.map} +0 -0
  856. /package/dist/{profile.spec-Z622PMSX.js.map → profile.spec-K2JOABV3.js.map} +0 -0
  857. /package/dist/{profileBarchart-3OCMQPHU.js.map → profileBarchart-IYWOBHGP.js.map} +0 -0
  858. /package/dist/{profileForms-QNS26EYF.js.map → profileForms-4VCEGMGS.js.map} +0 -0
  859. /package/dist/{profilePlot-E5LWDBSK.js.map → profilePlot-N246QTWM.js.map} +0 -0
  860. /package/dist/{profileRadar-JVISDMFQ.js.map → profileRadar-2ENLQG7V.js.map} +0 -0
  861. /package/dist/{profileRadarFacility-L3H7NERH.js.map → profileRadarFacility-FTNZELJ7.js.map} +0 -0
  862. /package/dist/{qualitative-7KOKJDCI.js.map → proteomeAbundance-AM4N7PLI.js.map} +0 -0
  863. /package/dist/{regression-H5SLMJTU.js.map → qualitative-I3GVVQ6U.js.map} +0 -0
  864. /package/dist/{regression.inputs-T4CB7HO6.js.map → regression-XBZL2KMJ.js.map} +0 -0
  865. /package/dist/{regression.inputs.term-CSO55NIV.js.map → regression.inputs-UCM5THYS.js.map} +0 -0
  866. /package/dist/{regression.inputs.values.table-3ORSYPRI.js.map → regression.inputs.term-24JWPAVV.js.map} +0 -0
  867. /package/dist/{regression.results-FVWF776Y.js.map → regression.inputs.values.table-QOHYUCIJ.js.map} +0 -0
  868. /package/dist/{regression.integration.spec-AODFYXEV.js.map → regression.integration.spec-JJXWPLID.js.map} +0 -0
  869. /package/dist/{sampleView-OCADT4BV.js.map → regression.results-T34IDQTC.js.map} +0 -0
  870. /package/dist/{regression.spec-D2SYDVSK.js.map → regression.spec-E74GPU5O.js.map} +0 -0
  871. /package/dist/{report-DBHQIHVX.js.map → report-U65OAFJR.js.map} +0 -0
  872. /package/dist/{sampleScatter.spec-NMQJ5WIE.js.map → sampleScatter.spec-3LFSRARK.js.map} +0 -0
  873. /package/dist/{singleCellCellType-OQEFL3EY.js.map → sampleView-MX7LX3EJ.js.map} +0 -0
  874. /package/dist/{samplelst-GWEMRR4J.js.map → samplelst-V4I6WIOC.js.map} +0 -0
  875. /package/dist/{samplematrix-QJ6PHCJ4.js.map → samplematrix-LNZJNTRE.js.map} +0 -0
  876. /package/dist/{sc-NVPIXDG2.js.map → sc-T2BPIFZ4.js.map} +0 -0
  877. /package/dist/{scatter-H7HUQRKE.js.map → scatter-PER7W2GO.js.map} +0 -0
  878. /package/dist/{selectGenomeWithTklst-W6FA72HM.js.map → selectGenomeWithTklst-UEJZV63V.js.map} +0 -0
  879. /package/dist/{singleCellGeneExpression-QPVTXR5W.js.map → singleCellCellType-OLXPVJE6.js.map} +0 -0
  880. /package/dist/{singleCellCellType.unit.spec-BAIWJSUP.js.map → singleCellCellType.unit.spec-MQH6HMRC.js.map} +0 -0
  881. /package/dist/{singleCellPlot-T2YNDBTX.js.map → singleCellGeneExpression-P2K6EAGJ.js.map} +0 -0
  882. /package/dist/{singleCellGeneExpression.unit.spec-Q5TS6VB5.js.map → singleCellGeneExpression.unit.spec-LMCCDVIY.js.map} +0 -0
  883. /package/dist/{snp-DAIHQXTJ.js.map → singleCellPlot-CP5QDUSH.js.map} +0 -0
  884. /package/dist/{singlecell-PAOWCTF5.js.map → singlecell-57YOSKNP.js.map} +0 -0
  885. /package/dist/{singlecell-B3NERPJ5.js.map → singlecell-FGDYQAVM.js.map} +0 -0
  886. /package/dist/{ssGSEA-5H4QBOY2.js.map → snp-BYMKURQO.js.map} +0 -0
  887. /package/dist/{snp.unit.spec-MXTEPR3Z.js.map → snp.unit.spec-6UGQYGQR.js.map} +0 -0
  888. /package/dist/{snplocus-PMAVBMTK.js.map → snplocus-AYSJ7PSU.js.map} +0 -0
  889. /package/dist/{spliceevent.a53ss.diagram-G6W7EY3Q.js.map → spliceevent.a53ss.diagram-BB73A4HM.js.map} +0 -0
  890. /package/dist/{spliceevent.exonskip.diagram-YHUNDN4M.js.map → spliceevent.exonskip.diagram-VWIAD5DQ.js.map} +0 -0
  891. /package/dist/{spliceevent.noeventdiagram-FN3PORQA.js.map → spliceevent.noeventdiagram-QACCAJS4.js.map} +0 -0
  892. /package/dist/{summarizeMutationDiagnosis-OAUXQ6HD.js.map → ssGSEA-REHCYQ7Z.js.map} +0 -0
  893. /package/dist/{ssGSEA.unit.spec-UBZGATIZ.js.map → ssGSEA.unit.spec-XJNHMFF5.js.map} +0 -0
  894. /package/dist/{summarizeCnvGeneexp-IR7HMUG3.js.map → summarizeCnvGeneexp-NDEEB7PV.js.map} +0 -0
  895. /package/dist/{summarizeGeneexpSurvival-INZXCZ37.js.map → summarizeGeneexpSurvival-ZCGBEB4C.js.map} +0 -0
  896. /package/dist/{summarizeMutationCnv-GZFJTCRN.js.map → summarizeMutationCnv-OOMN2AVW.js.map} +0 -0
  897. /package/dist/{summary-SAVKS777.js.map → summarizeMutationDiagnosis-B6TF3KU5.js.map} +0 -0
  898. /package/dist/{summarizeMutationSurvival-PT2BGPWD.js.map → summarizeMutationSurvival-Y2J6T2CS.js.map} +0 -0
  899. /package/dist/{survival-65IBMTWU.js.map → summary-O5LSGPWD.js.map} +0 -0
  900. /package/dist/{summary.integration.spec-LWO7Y4OP.js.map → summary.integration.spec-EH7FMP7B.js.map} +0 -0
  901. /package/dist/{summaryInput-SEIB7F3A.js.map → summaryInput-ZWURF7E2.js.map} +0 -0
  902. /package/dist/{sunburst-HCF2V66V.js.map → sunburst-ZDE5Q2SJ.js.map} +0 -0
  903. /package/dist/{termCollection-GYMOT2EE.js.map → survival-DTUOFMGJ.js.map} +0 -0
  904. /package/dist/{survival-RIV2T7KO.js.map → survival-XKLFNJF2.js.map} +0 -0
  905. /package/dist/{survival.integration.spec-2V2O4H7K.js.map → survival.integration.spec-J352BAT4.js.map} +0 -0
  906. /package/dist/{svgraph-XV52FOMN.js.map → svgraph-NZQ6Z4HS.js.map} +0 -0
  907. /package/dist/{svmr-BDAHM7UH.js.map → svmr-BPDWKVL2.js.map} +0 -0
  908. /package/dist/{table-5N2CRI36.js.map → table-6FOITCXA.js.map} +0 -0
  909. /package/dist/{tk-IOJVJ34S.js.map → termCollection-HFDUSCPL.js.map} +0 -0
  910. /package/dist/{termCollection-TZY6DOSP.js.map → termCollection-SWYRSREU.js.map} +0 -0
  911. /package/dist/{termCollection.unit.spec-VWHQ72DD.js.map → termCollection.unit.spec-ZSAAQS26.js.map} +0 -0
  912. /package/dist/{tvs.density-AQ5GD437.js.map → tk-D2YVENB3.js.map} +0 -0
  913. /package/dist/{tp.ui-JHPHESWM.js.map → tp.ui-XALNLDLX.js.map} +0 -0
  914. /package/dist/{tvs.dt-JPB46UPH.js.map → tvs.density-HSVPDDGA.js.map} +0 -0
  915. /package/dist/{tvs.numeric-PLNP7MBV.js.map → tvs.dt-TOZ47QR3.js.map} +0 -0
  916. /package/dist/{tvs.dtcnv.categorical-37TA7GCY.js.map → tvs.dtcnv.categorical-OZFNQFCX.js.map} +0 -0
  917. /package/dist/{tvs.dtcnv.continuous-X4K3RPYG.js.map → tvs.dtcnv.continuous-XCZJ7JOD.js.map} +0 -0
  918. /package/dist/{tvs.dtfusion-77SKDRRH.js.map → tvs.dtfusion-G3BI6YSH.js.map} +0 -0
  919. /package/dist/{tvs.dtsnvindel-2QGQ455S.js.map → tvs.dtsnvindel-ETMWTQLL.js.map} +0 -0
  920. /package/dist/{tvs.dtsv-QBCE5IHM.js.map → tvs.dtsv-66AEHBQE.js.map} +0 -0
  921. /package/dist/{violin-DCKEHIVC.js.map → tvs.numeric-AU4U3UXI.js.map} +0 -0
  922. /package/dist/{tvs.samplelst-NRSYJ64L.js.map → tvs.samplelst-TMUNONJI.js.map} +0 -0
  923. /package/dist/{tvs.termCollection-BK36KZL2.js.map → tvs.termCollection-HZ2ZVONI.js.map} +0 -0
  924. /package/dist/{violin.interactivity-RS6D5YPY.js.map → violin-P4A4BLKJ.js.map} +0 -0
  925. /package/dist/{violin.integration.spec-IIYDX5DT.js.map → violin.integration.spec-DSSHXEES.js.map} +0 -0
  926. /package/dist/{violin.renderer-XIQTOVEK.js.map → violin.interactivity-FRXW7MH4.js.map} +0 -0
  927. /package/dist/{vocabulary-6437MWB6.js.map → violin.renderer-LQAFOSRK.js.map} +0 -0
@@ -0,0 +1,423 @@
1
+ import {
2
+ getDefaultViolinSettings
3
+ } from "./chunk-OM22RN7S.js";
4
+ import {
5
+ getDefaultScatterSettings
6
+ } from "./chunk-OJSG5RK5.js";
7
+ import {
8
+ getDefaultBoxplotSettings
9
+ } from "./chunk-AXOTFMIM.js";
10
+ import {
11
+ PlotBase,
12
+ Tabs,
13
+ defaultUiLabels,
14
+ fillTermWrapper,
15
+ filterRxCompInit,
16
+ getDefaultBarSettings,
17
+ term0_term2_defaultQ
18
+ } from "./chunk-SAHCLNNL.js";
19
+ import {
20
+ importPlot
21
+ } from "./chunk-XEBPIJHM.js";
22
+ import {
23
+ Menu
24
+ } from "./chunk-CXMZYVZT.js";
25
+ import {
26
+ copyMerge,
27
+ getCompInit
28
+ } from "./chunk-MVTCBVSX.js";
29
+ import {
30
+ isNumericTerm
31
+ } from "./chunk-RTKRLATH.js";
32
+
33
+ // plots/summary.ts
34
+ var SummaryPlot = class _SummaryPlot extends PlotBase {
35
+ constructor(opts, api) {
36
+ super(opts, api);
37
+ this.components = {};
38
+ // expected class-specific props
39
+ this.chartsByType = {};
40
+ this.configTermKeys = ["term", "term0", "term2"];
41
+ this.type = _SummaryPlot.type;
42
+ this.dom = this.getDom(opts);
43
+ this.tabsData = this.getTabsData();
44
+ this.chartToggles = new Tabs({ holder: this.dom.chartToggles, tabs: this.tabsData, noContent: true });
45
+ this.components = {
46
+ plots: {}
47
+ };
48
+ }
49
+ static {
50
+ this.type = "summary";
51
+ }
52
+ preApiFreeze(api) {
53
+ api.getError = () => {
54
+ return this.error;
55
+ };
56
+ }
57
+ getDom(opts) {
58
+ const holder = opts.holder;
59
+ holder.header.style("padding", 0);
60
+ const paneTitleDiv = holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px");
61
+ return {
62
+ tip: new Menu({ padding: "0px" }),
63
+ holder,
64
+ body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
65
+ // will hold no data notice or the page title in multichart views
66
+ errdiv: holder.body.append("div").attr("class", "sja_errorbar").style("display", "none").style("padding", "5px"),
67
+ loading: holder.body.append("div").style("display", "none").style("padding", "5px").html("Loading ..."),
68
+ // dom.viz will hold the rendered view
69
+ viz: holder.body.append("div"),
70
+ plotDivs: {},
71
+ paneTitleDiv,
72
+ paneTitleText: paneTitleDiv.append("div").classed("sjpp-term-header", true).style("display", "inline-block").style("vertical-align", "sub"),
73
+ chartToggles: paneTitleDiv.append("div").style("display", "inline-block").style("margin-left", "10px"),
74
+ localRecoverDiv: paneTitleDiv.append("div").style("display", "inline-block"),
75
+ filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9)
76
+ };
77
+ }
78
+ getTabsData() {
79
+ const callback = (event, tab) => this.tabClickCallback(event, tab);
80
+ return [
81
+ {
82
+ childType: "barchart",
83
+ label: "Barchart",
84
+ isVisible: () => true,
85
+ disabled: () => false,
86
+ getConfig: async () => {
87
+ if (!this.config) return;
88
+ const config = { id: this.id, childType: "barchart" };
89
+ const { term, term2 } = this.config || {};
90
+ if (term) {
91
+ const mode = isNumericTerm(term?.term) ? "discrete" : term?.q.mode || "discrete";
92
+ config.term = await this.getWrappedTermCopy(term, mode);
93
+ }
94
+ if (term2) {
95
+ const mode = isNumericTerm(term2.term) ? "discrete" : term2.q.mode || "discrete";
96
+ config.term2 = await this.getWrappedTermCopy(term2, mode);
97
+ }
98
+ return config;
99
+ },
100
+ active: true,
101
+ callback
102
+ },
103
+ {
104
+ childType: "violin",
105
+ label: "Violin",
106
+ disabled: () => false,
107
+ isVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),
108
+ getConfig: async () => {
109
+ const term = this.config?.term;
110
+ const term2 = this.config.term2;
111
+ let _term, _term2;
112
+ this.violinContTerm = isNumericTerm(term?.term) ? "term" : "term2";
113
+ if (this.violinContTerm && this.violinContTerm === "term" || term.q?.mode == "continuous") {
114
+ _term = await this.getWrappedTermCopy(term, "continuous");
115
+ _term2 = await this.getWrappedTermCopy(term2, "discrete");
116
+ this.violinContTerm = "term";
117
+ } else if (this.violinContTerm && this.violinContTerm === "term2" || term2?.q?.mode == "continuous") {
118
+ _term = await this.getWrappedTermCopy(term, "discrete");
119
+ _term2 = await this.getWrappedTermCopy(term2, "continuous");
120
+ this.violinContTerm = "term2";
121
+ } else if (term2?.q?.mode == "discrete") {
122
+ _term = await this.getWrappedTermCopy(term, "discrete");
123
+ _term2 = await this.getWrappedTermCopy(term2, "continuous");
124
+ this.violinContTerm = "term2";
125
+ } else {
126
+ _term = await this.getWrappedTermCopy(term, "continuous");
127
+ _term2 = await this.getWrappedTermCopy(term2, "discrete");
128
+ this.violinContTerm = "term";
129
+ }
130
+ const config = { childType: "violin", term: _term, term2: _term2 };
131
+ return config;
132
+ },
133
+ active: false,
134
+ callback
135
+ },
136
+ {
137
+ childType: "boxplot",
138
+ label: "Boxplot",
139
+ disabled: () => false,
140
+ isVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),
141
+ getConfig: async () => {
142
+ const _term = this.config?.term;
143
+ const _term2 = this.config.term2;
144
+ let termMode = "continuous", term2Mode = "discrete";
145
+ this.boxContTerm = isNumericTerm(_term?.term) ? "term" : "term2";
146
+ if (this.boxContTerm && this.boxContTerm === "term" || _term.q?.mode == "continuous") {
147
+ termMode = "continuous";
148
+ term2Mode = "discrete";
149
+ this.boxContTerm = "term";
150
+ } else if (this.boxContTerm && this.boxContTerm === "term2" || _term2?.q?.mode == "continuous") {
151
+ termMode = "discrete";
152
+ term2Mode = "continuous";
153
+ this.boxContTerm = "term2";
154
+ } else if (_term2?.q?.mode == "discrete") {
155
+ termMode = "discrete";
156
+ term2Mode = "continuous";
157
+ this.boxContTerm = "term2";
158
+ }
159
+ const term = await this.getWrappedTermCopy(_term, termMode);
160
+ const term2 = await this.getWrappedTermCopy(_term2, term2Mode);
161
+ const config = {
162
+ childType: "boxplot",
163
+ term,
164
+ term2
165
+ };
166
+ return config;
167
+ },
168
+ active: false,
169
+ callback
170
+ },
171
+ {
172
+ childType: "sampleScatter",
173
+ label: "Scatter",
174
+ disabled: () => false,
175
+ isVisible: () => {
176
+ return isNumericTerm(this.config?.term.term) && isNumericTerm(this.config?.term2?.term);
177
+ },
178
+ getConfig: async () => {
179
+ const _term = await this.getWrappedTermCopy(this.config?.term, "continuous");
180
+ const _term2 = await this.getWrappedTermCopy(this.config?.term2, "continuous");
181
+ const config = {
182
+ childType: "sampleScatter",
183
+ term: _term,
184
+ term2: _term2,
185
+ groups: [],
186
+ term0: this.config.term0
187
+ };
188
+ return config;
189
+ },
190
+ active: false,
191
+ callback
192
+ }
193
+ ];
194
+ }
195
+ async init(appState) {
196
+ const state = this.getState(appState);
197
+ const config = structuredClone(state.config);
198
+ this.initUi(this.opts, config);
199
+ this.components.filter = await filterRxCompInit({
200
+ app: this.app,
201
+ vocabApi: this.app.vocabApi,
202
+ parentId: this.id,
203
+ holder: this.dom.filterDiv,
204
+ hideLabel: true,
205
+ emptyLabel: "+Add new filter",
206
+ callback: (filter) => {
207
+ this.app.dispatch({
208
+ id: this.id,
209
+ type: "plot_edit",
210
+ config: { filter }
211
+ });
212
+ }
213
+ });
214
+ }
215
+ reactsTo(action) {
216
+ if (action.type.includes("cache_termq")) return true;
217
+ if (action.type.startsWith("plot_")) {
218
+ if (action.type.startsWith("plot_")) {
219
+ return action.id === this.id || action.id == this.parentId;
220
+ }
221
+ }
222
+ if (action.type.startsWith("filter")) return true;
223
+ if (action.type.startsWith("cohort")) return true;
224
+ if (action.type == "app_refresh") return true;
225
+ return false;
226
+ }
227
+ getState(appState) {
228
+ const config = appState.plots.find((p) => p.id === this.id);
229
+ if (!config) {
230
+ throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
231
+ }
232
+ return {
233
+ termfilter: appState.termfilter,
234
+ config,
235
+ // quick fix to skip history tracking as needed
236
+ _scope_: appState._scope_
237
+ };
238
+ }
239
+ async main() {
240
+ delete this.error;
241
+ this.dom.errdiv.style("display", "none").html("");
242
+ this.dom.loading.style("display", "");
243
+ this.config = await this.getMutableConfig();
244
+ this.maySetSandboxHeader();
245
+ if (!this.components.plots[this.config.childType]) {
246
+ await this.setComponent(this.config);
247
+ }
248
+ this.dom.loading.style("display", "none");
249
+ this.render();
250
+ const activeTabIndex = this.tabsData.findIndex((tab) => tab.childType == this.config.childType);
251
+ this.chartToggles.update(activeTabIndex);
252
+ const numVisTabs = this.tabsData.filter((d) => d.isVisible()).length;
253
+ if (numVisTabs > 1) this.dom.chartToggles.style("display", "inline-block");
254
+ else this.dom.chartToggles.style("display", "none");
255
+ }
256
+ maySetSandboxHeader() {
257
+ const { term, term2 } = this.config;
258
+ const mainTerm = term.getTitleText?.() || term.term.name;
259
+ if (term2?.type) {
260
+ this.dom.paneTitleText.html(
261
+ `${term2.getTitleText?.() || term2.term.name} vs ${mainTerm}` + (this.config.assayCohortTitle ? ` (${this.config.assayCohortTitle})` : "")
262
+ );
263
+ } else {
264
+ this.dom.paneTitleText.html(mainTerm + (this.config.assayCohortTitle ? ` (${this.config.assayCohortTitle})` : ""));
265
+ }
266
+ }
267
+ async setComponent(config) {
268
+ const _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`);
269
+ this.dom.plotDivs[config.childType] = this.dom.viz.append("div");
270
+ this.components.plots[config.childType] = await _.componentInit({
271
+ app: this.app,
272
+ holder: this.dom.plotDivs[config.childType],
273
+ id: this.id,
274
+ parent: this.api
275
+ });
276
+ }
277
+ destroy() {
278
+ this.dom.holder.app_div.selectAll("*").remove();
279
+ this.dom.holder.app_div.remove();
280
+ for (const key in this.dom) {
281
+ delete this.dom[key];
282
+ }
283
+ }
284
+ initUi(opts, config) {
285
+ this.dom.paneTitleText.html(config.term.term.name);
286
+ this.chartToggles.main();
287
+ }
288
+ async tabClickCallback(event, tab) {
289
+ if (!tab || !tab.getConfig) return;
290
+ let config;
291
+ try {
292
+ this.dom.viz.style("display", "none");
293
+ this.dom.loading.style("display", "");
294
+ config = await tab.getConfig();
295
+ this.dom.loading.style("display", "none");
296
+ this.dom.viz.style("display", "");
297
+ if (config)
298
+ this.app.dispatch({
299
+ type: "plot_edit",
300
+ id: this.id,
301
+ config
302
+ });
303
+ } catch (e) {
304
+ this.dom.loading.style("display", "none");
305
+ this.error = e;
306
+ this.dom.errdiv.style("display", "").html(`Error: ${e.message || e.error || e}`);
307
+ }
308
+ }
309
+ async getWrappedTermCopy(term, mode) {
310
+ if (!term) return;
311
+ const tw = structuredClone(term);
312
+ tw.q.mode = mode;
313
+ await fillTermWrapper(tw, this.app.vocabApi);
314
+ return tw;
315
+ }
316
+ render() {
317
+ for (const childType of Object.keys(this.components.plots)) {
318
+ const chart = this.components.plots[childType];
319
+ if (chart.type != this.config.childType) {
320
+ this.dom.plotDivs[chart.type].style("display", "none");
321
+ }
322
+ }
323
+ this.dom.plotDivs[this.config.childType].style("display", "");
324
+ }
325
+ getChartImages() {
326
+ const chart = this.components.plots[this.config.childType];
327
+ if (chart?.getChartImages) {
328
+ return chart.getChartImages();
329
+ }
330
+ return null;
331
+ }
332
+ };
333
+ var summaryInit = getCompInit(SummaryPlot);
334
+ var componentInit = summaryInit;
335
+ async function getPlotConfig(opts, app) {
336
+ if (!opts.term) throw "summary getPlotConfig: opts.term{} missing";
337
+ try {
338
+ opts.term = await fillTermWrapper(
339
+ opts.term,
340
+ app.vocabApi,
341
+ opts.term.q || { geneVariant: { type: "predefined-groupset" } }
342
+ );
343
+ if (opts.term2)
344
+ opts.term2 = await fillTermWrapper(
345
+ opts.term2,
346
+ app.vocabApi,
347
+ opts.term2.bins || opts.term2.q ? void 0 : term0_term2_defaultQ
348
+ );
349
+ if (opts.term0)
350
+ opts.term0 = await fillTermWrapper(
351
+ opts.term0,
352
+ app.vocabApi,
353
+ opts.term0.bins || opts.term0.q ? void 0 : term0_term2_defaultQ
354
+ );
355
+ if (opts.colorTW) opts.colorTW = await fillTermWrapper(opts.colorTW, app.vocabApi);
356
+ if (opts.shapeTW) opts.shapeTW = await fillTermWrapper(opts.shapeTW, app.vocabApi);
357
+ if (opts.scaleDotTW) opts.scaleDotTW = await fillTermWrapper(opts.scaleDotTW, app.vocabApi);
358
+ } catch (e) {
359
+ if (e.stack) console.log(e.stack);
360
+ throw `${e} [summary getPlotConfig()]`;
361
+ }
362
+ const config = {
363
+ chartType: "summary",
364
+ childType: "barchart",
365
+ //id: opts.term.term.id,
366
+ term: opts.term,
367
+ groups: [],
368
+ controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
369
+ settings: {
370
+ controls: {
371
+ isOpen: false
372
+ },
373
+ common: {
374
+ use_logscale: false,
375
+ // flag for y-axis scale type, 0=linear, 1=log
376
+ use_percentage: false
377
+ // Move to barchart settings
378
+ // barheight: 300, // maximum bar length
379
+ // barwidth: 20, // bar thickness
380
+ // barspace: 2 // space between two bars
381
+ },
382
+ barchart: getDefaultBarSettings(app),
383
+ violin: getDefaultViolinSettings(app),
384
+ boxplot: getDefaultBoxplotSettings(app),
385
+ sampleScatter: getDefaultScatterSettings(opts)
386
+ },
387
+ mayAdjustConfig(config2, edits = {}) {
388
+ if (edits.childType) {
389
+ if (config2.childType != edits.childType)
390
+ throw `action.config.childType was not applied in mass store.plot_edit()`;
391
+ return;
392
+ }
393
+ if (config2.term?.q?.mode == "continuous" && config2.term2?.q?.mode == "continuous") {
394
+ config2.childType = "sampleScatter";
395
+ } else if (config2.term?.term?.type == "termCollection") {
396
+ config2.childType = config2.term.term?.memberType == "numeric" ? "violin" : "barchart";
397
+ } else if (config2.term?.q?.mode == "continuous" || config2.term2?.q?.mode == "continuous") {
398
+ if (!discreteByContinuousPlots.has(config2.childType)) {
399
+ if (opts.childType && !discreteByContinuousPlots.has(opts.childType)) {
400
+ console.warn(
401
+ `ignoring summary opts.childType='${opts.childType}' since it does not support plotting discrete by continuous tw's`
402
+ );
403
+ config2.childType = "violin";
404
+ } else {
405
+ config2.childType = opts.childType || "violin";
406
+ }
407
+ }
408
+ } else {
409
+ config2.childType = "barchart";
410
+ }
411
+ }
412
+ };
413
+ if (config.term.term.type == "geneVariant") config.settings.barchart.colorBars = true;
414
+ return copyMerge(config, opts);
415
+ }
416
+ var discreteByContinuousPlots = /* @__PURE__ */ new Set(["violin", "boxplot"]);
417
+
418
+ export {
419
+ summaryInit,
420
+ componentInit,
421
+ getPlotConfig
422
+ };
423
+ //# sourceMappingURL=chunk-7Q5X253Q.js.map
@@ -0,0 +1,7 @@
1
+ {
2
+ "version": 3,
3
+ "sources": ["../plots/summary.ts"],
4
+ "sourcesContent": ["import { getCompInit, copyMerge, type ComponentApi, type RxComponent } from '#rx'\nimport { PlotBase, defaultUiLabels } from './PlotBase.ts'\nimport { Menu, Tabs } from '#dom'\nimport { fillTermWrapper } from '#termsetting'\n// import { recoverInit } from '../rx/src/recover'\nimport { getDefaultViolinSettings } from './violin.js'\nimport { getDefaultBarSettings } from './barchart.js'\nimport { getDefaultBoxplotSettings } from './boxplot/defaults'\nimport { getDefaultScatterSettings } from './scatter/settings/defaults'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { term0_term2_defaultQ } from './controls'\nimport { importPlot } from './importPlot.js'\nimport { filterRxCompInit } from '#filter'\n\nclass SummaryPlot extends PlotBase implements RxComponent {\n\tstatic type = 'summary'\n\n\t// expected RxComponent props, some are already declared/set in PlotBase\n\ttype: string\n\tparentId?: string\n\tdom!: {\n\t\t[index: string]: any\n\t}\n\tcomponents: {\n\t\t[name: string]: ComponentApi | { [name: string]: ComponentApi }\n\t} = {}\n\n\terror: any\n\n\t// expected class-specific props\n\tchartsByType: { [chartType: string]: ComponentApi } = {}\n\tconfigTermKeys = ['term', 'term0', 'term2']\n\tconfig: any\n\ttabsData: any[]\n\tchartToggles: Tabs\n\n\tviolinContTerm?: 'term' | 'term2'\n\tboxContTerm?: 'term' | 'term2'\n\n\tconstructor(opts, api) {\n\t\tsuper(opts, api)\n\t\tthis.type = SummaryPlot.type\n\t\tthis.dom = this.getDom(opts)\n\t\tthis.tabsData = this.getTabsData()\n\t\tthis.chartToggles = new Tabs({ holder: this.dom.chartToggles, tabs: this.tabsData, noContent: true })\n\t\tthis.components = {\n\t\t\tplots: {}\n\t\t}\n\t}\n\n\tpreApiFreeze(api) {\n\t\tapi.getError = () => {\n\t\t\treturn this.error\n\t\t}\n\t}\n\n\tgetDom(opts) {\n\t\tconst holder = opts.holder\n\t\tholder.header.style('padding', 0)\n\n\t\tconst paneTitleDiv = holder.header\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('color', '#555') // changed from #999 to address Section 508 contrast issue\n\t\t\t.style('padding-left', '7px')\n\n\t\treturn {\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tholder,\n\t\t\tbody: holder.body\n\t\t\t\t// .style('margin-top', '-1px')\n\t\t\t\t.style('white-space', 'nowrap')\n\t\t\t\t.style('overflow-x', 'auto'),\n\n\t\t\t// will hold no data notice or the page title in multichart views\n\t\t\terrdiv: holder.body.append('div').attr('class', 'sja_errorbar').style('display', 'none').style('padding', '5px'),\n\n\t\t\tloading: holder.body.append('div').style('display', 'none').style('padding', '5px').html('Loading ...'),\n\n\t\t\t// dom.viz will hold the rendered view\n\t\t\tviz: holder.body.append('div'),\n\t\t\tplotDivs: {},\n\t\t\tpaneTitleDiv,\n\t\t\tpaneTitleText: paneTitleDiv\n\t\t\t\t.append('div')\n\t\t\t\t.classed('sjpp-term-header', true)\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('vertical-align', 'sub'),\n\t\t\tchartToggles: paneTitleDiv.append('div').style('display', 'inline-block').style('margin-left', '10px'),\n\t\t\tlocalRecoverDiv: paneTitleDiv.append('div').style('display', 'inline-block'),\n\t\t\tfilterDiv: holder.header.append('div').style('display', 'inline-block').style('zoom', 0.9)\n\t\t}\n\t}\n\n\tgetTabsData() {\n\t\tconst callback = (event, tab) => this.tabClickCallback(event, tab)\n\t\treturn [\n\t\t\t{\n\t\t\t\tchildType: 'barchart',\n\t\t\t\tlabel: 'Barchart',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tdisabled: () => false,\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tif (!this.config) return\n\t\t\t\t\tconst config: any = { id: this.id, childType: 'barchart' }\n\t\t\t\t\tconst { term, term2 } = this.config || {}\n\t\t\t\t\tif (term) {\n\t\t\t\t\t\tconst mode = isNumericTerm(term?.term) ? 'discrete' : term?.q.mode || 'discrete'\n\t\t\t\t\t\tconfig.term = await this.getWrappedTermCopy(term, mode)\n\t\t\t\t\t}\n\t\t\t\t\tif (term2) {\n\t\t\t\t\t\tconst mode = isNumericTerm(term2.term) ? 'discrete' : term2.q.mode || 'discrete'\n\t\t\t\t\t\tconfig.term2 = await this.getWrappedTermCopy(term2, mode)\n\t\t\t\t\t}\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: true,\n\t\t\t\tcallback\n\t\t\t},\n\t\t\t{\n\t\t\t\tchildType: 'violin',\n\t\t\t\tlabel: 'Violin',\n\t\t\t\tdisabled: () => false,\n\t\t\t\tisVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tconst term = this.config?.term\n\t\t\t\t\tconst term2 = this.config.term2\n\n\t\t\t\t\tlet _term, _term2\n\t\t\t\t\tthis.violinContTerm = isNumericTerm(term?.term) ? 'term' : 'term2'\n\n\t\t\t\t\t//If the first term was continuous or is coming as continuous\n\t\t\t\t\tif ((this.violinContTerm && this.violinContTerm === 'term') || term.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from scatter plot\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'continuous')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'discrete')\n\t\t\t\t\t\tthis.violinContTerm = 'term'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term was continuous or is coming as continuous\n\t\t\t\t\telse if ((this.violinContTerm && this.violinContTerm === 'term2') || term2?.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'discrete')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'continuous')\n\t\t\t\t\t\tthis.violinContTerm = 'term2'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term is coming as discrete from the scatter\n\t\t\t\t\telse if (term2?.q?.mode == 'discrete') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'discrete')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'continuous')\n\t\t\t\t\t\tthis.violinContTerm = 'term2'\n\t\t\t\t\t}\n\t\t\t\t\t//by default\n\t\t\t\t\telse {\n\t\t\t\t\t\t_term = await this.getWrappedTermCopy(term, 'continuous')\n\t\t\t\t\t\t_term2 = await this.getWrappedTermCopy(term2, 'discrete')\n\t\t\t\t\t\tthis.violinContTerm = 'term'\n\t\t\t\t\t}\n\t\t\t\t\tconst config = { childType: 'violin', term: _term, term2: _term2 }\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: false,\n\t\t\t\tcallback\n\t\t\t},\n\t\t\t{\n\t\t\t\tchildType: 'boxplot',\n\t\t\t\tlabel: 'Boxplot',\n\t\t\t\tdisabled: () => false,\n\t\t\t\tisVisible: () => isNumericTerm(this.config?.term?.term) || isNumericTerm(this.config?.term2?.term),\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tconst _term = this.config?.term\n\t\t\t\t\tconst _term2 = this.config.term2\n\n\t\t\t\t\tlet termMode = 'continuous',\n\t\t\t\t\t\tterm2Mode = 'discrete'\n\t\t\t\t\tthis.boxContTerm = isNumericTerm(_term?.term) ? 'term' : 'term2'\n\n\t\t\t\t\t//If the first term was continuous or is coming as continuous\n\t\t\t\t\tif ((this.boxContTerm && this.boxContTerm === 'term') || _term.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from scatter plot\n\t\t\t\t\t\ttermMode = 'continuous'\n\t\t\t\t\t\tterm2Mode = 'discrete'\n\t\t\t\t\t\tthis.boxContTerm = 'term'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term was continuous or is coming as continuous\n\t\t\t\t\telse if ((this.boxContTerm && this.boxContTerm === 'term2') || _term2?.q?.mode == 'continuous') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\ttermMode = 'discrete'\n\t\t\t\t\t\tterm2Mode = 'continuous'\n\t\t\t\t\t\tthis.boxContTerm = 'term2'\n\t\t\t\t\t}\n\t\t\t\t\t//If the second term is coming as discrete from the scatter\n\t\t\t\t\telse if (_term2?.q?.mode == 'discrete') {\n\t\t\t\t\t\t// must mean coming from barchart\n\t\t\t\t\t\ttermMode = 'discrete'\n\t\t\t\t\t\tterm2Mode = 'continuous'\n\t\t\t\t\t\tthis.boxContTerm = 'term2'\n\t\t\t\t\t}\n\n\t\t\t\t\tconst term = await this.getWrappedTermCopy(_term, termMode)\n\t\t\t\t\tconst term2 = await this.getWrappedTermCopy(_term2, term2Mode)\n\t\t\t\t\tconst config = {\n\t\t\t\t\t\tchildType: 'boxplot',\n\t\t\t\t\t\tterm,\n\t\t\t\t\t\tterm2\n\t\t\t\t\t}\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: false,\n\t\t\t\tcallback\n\t\t\t},\n\t\t\t{\n\t\t\t\tchildType: 'sampleScatter',\n\t\t\t\tlabel: 'Scatter',\n\t\t\t\tdisabled: () => false,\n\t\t\t\tisVisible: () => {\n\t\t\t\t\treturn isNumericTerm(this.config?.term.term) && isNumericTerm(this.config?.term2?.term)\n\t\t\t\t},\n\t\t\t\tgetConfig: async () => {\n\t\t\t\t\tconst _term = await this.getWrappedTermCopy(this.config?.term, 'continuous')\n\t\t\t\t\tconst _term2 = await this.getWrappedTermCopy(this.config?.term2, 'continuous')\n\t\t\t\t\tconst config = {\n\t\t\t\t\t\tchildType: 'sampleScatter',\n\t\t\t\t\t\tterm: _term,\n\t\t\t\t\t\tterm2: _term2,\n\t\t\t\t\t\tgroups: [],\n\t\t\t\t\t\tterm0: this.config.term0\n\t\t\t\t\t}\n\t\t\t\t\treturn config\n\t\t\t\t},\n\t\t\t\tactive: false,\n\t\t\t\tcallback\n\t\t\t}\n\t\t]\n\t}\n\n\tasync init(appState) {\n\t\tconst state = this.getState(appState)\n\t\tconst config = structuredClone(state.config)\n\t\tthis.initUi(this.opts, config)\n\n\t\t// this.components.recover = await recoverInit({\n\t\t// \tapp: this.app,\n\t\t// \tholder: this.dom.localRecoverDiv,\n\t\t// \tgetState: appState => this.getState(appState),\n\t\t// \treactsTo: action => action.id == this.id && action.type == 'plot_edit' && action._scope_ != 'none',\n\t\t// \tplot_id: this.id,\n\t\t// \tmaxHistoryLen: 10,\n\t\t// \tmargin: '5px 10px' //Prevents a gap appearing between the tabs and sandbox content\n\t\t// })\n\t\tthis.components.filter = await filterRxCompInit({\n\t\t\tapp: this.app,\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tparentId: this.id,\n\t\t\tholder: this.dom.filterDiv,\n\t\t\thideLabel: true,\n\n\t\t\temptyLabel: '+Add new filter',\n\t\t\tcallback: filter => {\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\tid: this.id,\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tconfig: { filter }\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.includes('cache_termq')) return true\n\t\tif (action.type.startsWith('plot_')) {\n\t\t\tif (action.type.startsWith('plot_')) {\n\t\t\t\treturn action.id === this.id || action.id == this.parentId\n\t\t\t}\n\t\t}\n\t\tif (action.type.startsWith('filter')) return true\n\t\tif (action.type.startsWith('cohort')) return true\n\t\tif (action.type == 'app_refresh') return true\n\t\treturn false\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\ttermfilter: appState.termfilter,\n\t\t\tconfig,\n\t\t\t// quick fix to skip history tracking as needed\n\t\t\t_scope_: appState._scope_\n\t\t}\n\t}\n\n\tasync main() {\n\t\tdelete this.error\n\t\tthis.dom.errdiv.style('display', 'none').html('')\n\t\tthis.dom.loading.style('display', '')\n\n\t\tthis.config = await this.getMutableConfig()\n\t\tthis.maySetSandboxHeader()\n\n\t\tif (!this.components.plots[this.config.childType]) {\n\t\t\tawait this.setComponent(this.config)\n\t\t}\n\n\t\tthis.dom.loading.style('display', 'none')\n\t\tthis.render()\n\n\t\tconst activeTabIndex = this.tabsData.findIndex(tab => tab.childType == this.config.childType)\n\t\tthis.chartToggles.update(activeTabIndex)\n\n\t\t//Only show tabs when more than one are present\n\t\tconst numVisTabs = this.tabsData.filter(d => d.isVisible()).length\n\t\tif (numVisTabs > 1) this.dom.chartToggles.style('display', 'inline-block')\n\t\telse this.dom.chartToggles.style('display', 'none')\n\t}\n\n\tmaySetSandboxHeader() {\n\t\tconst { term, term2 } = this.config\n\t\tconst mainTerm = term.getTitleText?.() || term.term.name\n\t\tif (term2?.type) {\n\t\t\tthis.dom.paneTitleText.html(\n\t\t\t\t`${term2.getTitleText?.() || term2.term.name} vs ${mainTerm}` +\n\t\t\t\t\t(this.config.assayCohortTitle ? ` (${this.config.assayCohortTitle})` : '')\n\t\t\t)\n\t\t} else {\n\t\t\tthis.dom.paneTitleText.html(mainTerm + (this.config.assayCohortTitle ? ` (${this.config.assayCohortTitle})` : ''))\n\t\t}\n\t}\n\n\tasync setComponent(config) {\n\t\t// !!! quick fix for rollup to bundle,\n\t\t// will eventually need to move to a subnested folder structure\n\t\tconst _ = await importPlot(config.childType, `unsupported childType='${config.childType}'`)\n\t\tthis.dom.plotDivs[config.childType] = this.dom.viz.append('div')\n\n\t\t// assumes only 1 chart per chartType would be rendered in the summary sandbox\n\t\tthis.components.plots[config.childType] = await _.componentInit({\n\t\t\tapp: this.app,\n\t\t\tholder: this.dom.plotDivs[config.childType],\n\t\t\tid: this.id,\n\t\t\tparent: this.api\n\t\t})\n\t}\n\n\tdestroy() {\n\t\t// the dom.holder itself is not a d3-selection,\n\t\t// so need to specify a destroy function here\n\t\t// since the default rx.componentApi.destroy()\n\t\t// does not work when dom.holder is not a d3-selection\n\t\tthis.dom.holder.app_div.selectAll('*').remove()\n\t\tthis.dom.holder.app_div.remove()\n\t\tfor (const key in this.dom) {\n\t\t\tdelete this.dom[key]\n\t\t}\n\t}\n\n\tinitUi(opts, config) {\n\t\tthis.dom.paneTitleText.html(config.term.term.name)\n\t\tthis.chartToggles.main()\n\t}\n\n\tasync tabClickCallback(event, tab) {\n\t\tif (!tab || !tab.getConfig) return\n\t\tlet config\n\t\ttry {\n\t\t\tthis.dom.viz.style('display', 'none')\n\t\t\tthis.dom.loading.style('display', '')\n\t\t\tconfig = await tab.getConfig()\n\t\t\tthis.dom.loading.style('display', 'none')\n\t\t\tthis.dom.viz.style('display', '')\n\t\t\tif (config)\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: config\n\t\t\t\t})\n\t\t} catch (e: any) {\n\t\t\tthis.dom.loading.style('display', 'none')\n\t\t\tthis.error = e\n\t\t\tthis.dom.errdiv.style('display', '').html(`Error: ${e.message || e.error || e}`)\n\t\t}\n\t}\n\n\tasync getWrappedTermCopy(term, mode) {\n\t\tif (!term) return\n\t\tconst tw = structuredClone(term)\n\t\t// TODO: this is not type safe, assumes any q{} can be set to any mode\n\t\ttw.q.mode = mode // {mode, isAtomic: true}\n\t\t// If tw.q is empty/undefined, the default q\n\t\t// will be assigned by fillTw by term type\n\t\tawait fillTermWrapper(tw, this.app.vocabApi)\n\t\treturn tw\n\t}\n\n\trender() {\n\t\tfor (const childType of Object.keys(this.components.plots)) {\n\t\t\tconst chart = this.components.plots[childType]\n\t\t\t// hide non-active charts first, so not to momentarily have two visible charts\n\t\t\tif (chart.type != this.config.childType) {\n\t\t\t\tthis.dom.plotDivs[chart.type].style('display', 'none')\n\t\t\t}\n\t\t}\n\n\t\tthis.dom.plotDivs[this.config.childType].style('display', '')\n\t}\n\n\tgetChartImages() {\n\t\tconst chart = this.components.plots[this.config.childType]\n\t\tif (chart?.getChartImages) {\n\t\t\treturn chart.getChartImages()\n\t\t}\n\t\treturn null\n\t}\n}\n\nexport const summaryInit = getCompInit(SummaryPlot)\nexport const componentInit = summaryInit\n\nexport async function getPlotConfig(opts, app) {\n\tif (!opts.term) throw 'summary getPlotConfig: opts.term{} missing'\n\ttry {\n\t\topts.term = await fillTermWrapper(\n\t\t\topts.term,\n\t\t\tapp.vocabApi,\n\t\t\topts.term.q || { geneVariant: { type: 'predefined-groupset' } }\n\t\t)\n\t\t// supply term0_term2_defaultQ if opts.term0/2.bins/q is undefined\n\t\t// e.g. for scatterplot, opts.term2.q.mode='continuous' so will not\n\t\t// want to override with q.mode from term0_term2_defaultQ\n\t\tif (opts.term2)\n\t\t\topts.term2 = await fillTermWrapper(\n\t\t\t\topts.term2,\n\t\t\t\tapp.vocabApi,\n\t\t\t\topts.term2.bins || opts.term2.q ? undefined : term0_term2_defaultQ\n\t\t\t)\n\t\tif (opts.term0)\n\t\t\topts.term0 = await fillTermWrapper(\n\t\t\t\topts.term0,\n\t\t\t\tapp.vocabApi,\n\t\t\t\topts.term0.bins || opts.term0.q ? undefined : term0_term2_defaultQ\n\t\t\t)\n\t\t// dynamic scatterplot is a child type of summary and following args are possible; if present, initialize them\n\t\tif (opts.colorTW) opts.colorTW = await fillTermWrapper(opts.colorTW, app.vocabApi)\n\t\tif (opts.shapeTW) opts.shapeTW = await fillTermWrapper(opts.shapeTW, app.vocabApi)\n\t\tif (opts.scaleDotTW) opts.scaleDotTW = await fillTermWrapper(opts.scaleDotTW, app.vocabApi)\n\t} catch (e: any) {\n\t\tif (e.stack) console.log(e.stack)\n\t\tthrow `${e} [summary getPlotConfig()]`\n\t}\n\n\tconst config = {\n\t\tchartType: 'summary',\n\t\tchildType: 'barchart',\n\t\t//id: opts.term.term.id,\n\t\tterm: opts.term,\n\t\tgroups: [],\n\t\tcontrolLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),\n\t\tsettings: {\n\t\t\tcontrols: {\n\t\t\t\tisOpen: false\n\t\t\t},\n\t\t\tcommon: {\n\t\t\t\tuse_logscale: false, // flag for y-axis scale type, 0=linear, 1=log\n\t\t\t\tuse_percentage: false\n\t\t\t\t// Move to barchart settings\n\t\t\t\t// barheight: 300, // maximum bar length\n\t\t\t\t// barwidth: 20, // bar thickness\n\t\t\t\t// barspace: 2 // space between two bars\n\t\t\t},\n\n\t\t\tbarchart: getDefaultBarSettings(app),\n\n\t\t\tviolin: getDefaultViolinSettings(app),\n\n\t\t\tboxplot: getDefaultBoxplotSettings(app),\n\n\t\t\tsampleScatter: getDefaultScatterSettings(opts)\n\t\t},\n\t\tmayAdjustConfig(config, edits: { childType?: string } = {}) {\n\t\t\t/*\n\t\t\t\twhen recovering from state rehydration:\n\t\t\t\t- Mass store must call mayAdjustConfig(), if available, since the recovered state\n\t\t\t\tmay be partial such as from an example url. Even a previously saved \"full\" state\n\t\t\t\tmay still need to be filled or reshaped with new state config/settings.\n\t\t\t*/\n\n\t\t\tif (edits.childType) {\n\t\t\t\t// no need to set config.childType if a value is already specified\n\t\t\t\t// in an edits object (optional second argument), as processed by mass store\n\t\t\t\tif (config.childType != edits.childType)\n\t\t\t\t\tthrow `action.config.childType was not applied in mass store.plot_edit()`\n\t\t\t\treturn\n\t\t\t}\n\t\t\t// config.childType may be stale, OR edits.childType may not be available,\n\t\t\t// when the summary plot_edit is triggered by replacing a term, such as replacing\n\t\t\t// categorical overlay with numeric, in which case the dispatched action might not\n\t\t\t// know in advance what the chiltType should be. It is much more reliable and consistent\n\t\t\t// to determine the default plots here, depending on the processed config.\n\t\t\tif (config.term?.q?.mode == 'continuous' && config.term2?.q?.mode == 'continuous') {\n\t\t\t\t// TODO: may need more logic later if more than one summary childType,\n\t\t\t\t// besides scatter, can support 2 continuous terms\n\t\t\t\tconfig.childType = 'sampleScatter'\n\t\t\t} else if (config.term?.term?.type == 'termCollection') {\n\t\t\t\t// TODO: may need more logic later if more than one summary childType,\n\t\t\t\t// besides barchart, can support discrete tw only\n\t\t\t\tconfig.childType = config.term.term?.memberType == 'numeric' ? 'violin' : 'barchart'\n\t\t\t} else if (config.term?.q?.mode == 'continuous' || config.term2?.q?.mode == 'continuous') {\n\t\t\t\tif (!discreteByContinuousPlots.has(config.childType)) {\n\t\t\t\t\t// only change config.childType if the current value is not supported by discrete + continuous tw\n\t\t\t\t\tif (opts.childType && !discreteByContinuousPlots.has(opts.childType)) {\n\t\t\t\t\t\tconsole.warn(\n\t\t\t\t\t\t\t`ignoring summary opts.childType='${opts.childType}' since it does not support plotting discrete by continuous tw's`\n\t\t\t\t\t\t)\n\t\t\t\t\t\tconfig.childType = 'violin'\n\t\t\t\t\t} else {\n\t\t\t\t\t\tconfig.childType = opts.childType || 'violin'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// TODO: may need more logic later if more than one summary childType,\n\t\t\t\t// besides barchart, can support discrete tw only\n\t\t\t\tconfig.childType = 'barchart'\n\t\t\t}\n\t\t}\n\t}\n\t//config.mayAdjustConfig(config)\n\n\t// TODO: may do similar thing for custom term\n\tif (config.term.term.type == 'geneVariant') config.settings.barchart.colorBars = true\n\n\t// may apply term-specific changes to the default object\n\treturn copyMerge(config, opts)\n}\n\nconst discreteByContinuousPlots = new Set(['violin', 'boxplot'])\n"],
5
+ "mappings": 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6
+ "names": ["config"]
7
+ }
@@ -0,0 +1,170 @@
1
+ import {
2
+ getEmptyCell,
3
+ maySetEmptyCell,
4
+ setCellProps
5
+ } from "./chunk-Z5XHVPCP.js";
6
+ import {
7
+ TermTypeGroups
8
+ } from "./chunk-SOYDFNWV.js";
9
+ import {
10
+ __export
11
+ } from "./chunk-HFNDKYVF.js";
12
+
13
+ // plots/matrix/matrix.serieses.js
14
+ var matrix_serieses_exports = {};
15
+ __export(matrix_serieses_exports, {
16
+ getSerieses: () => getSerieses
17
+ });
18
+ function getSerieses(data) {
19
+ const s = this.settings.matrix;
20
+ const serieses = [];
21
+ const { colw, dx, dy, xMin, xMax } = this.dimensions;
22
+ const dvt = this.config.divideBy || {};
23
+ const divideByTermId = "id" in dvt ? dvt.id : dvt.name;
24
+ const legendGroups = {};
25
+ this.colorScaleByTermId = {};
26
+ for (const t of this.termOrder) {
27
+ const $id = t.tw.$id;
28
+ const termid = "id" in t.tw.term ? t.tw.term.id : t.tw.term.name;
29
+ const isDivideByTerm = termid === divideByTermId;
30
+ const emptyGridCells = [];
31
+ const cellht = t.grp.type == "hierCluster" ? s.clusterRowh : dy;
32
+ const htAdjust = t.grp.type == "hierCluster" ? 0 : t.totalHtAdjustments;
33
+ const y = s.transpose ? 0 : t.totalIndex * cellht + t.visibleGrpIndex * s.rowgspace + htAdjust;
34
+ const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
35
+ const hoverY0 = (twSpecificSettings[$id]?.contBarGap || 0) + y;
36
+ const series = {
37
+ t,
38
+ tw: t.tw,
39
+ cells: [],
40
+ y,
41
+ hoverY0,
42
+ hoverY1: hoverY0 + (twSpecificSettings[$id]?.contBarH || cellht)
43
+ };
44
+ for (const so of this.unfilteredSampleOrder) {
45
+ const { totalIndex, grpIndex, row } = so;
46
+ series.x = !s.transpose ? 0 : t.totalIndex * dx + t.visibleGrpIndex * s.colgspace;
47
+ const anno = row[$id];
48
+ const cellTemplate = {
49
+ s: so,
50
+ sample: row.sample,
51
+ tw: t.tw,
52
+ term: t.tw.term,
53
+ termid,
54
+ $id,
55
+ totalIndex,
56
+ grpIndex,
57
+ row,
58
+ t,
59
+ seriesY: y
60
+ };
61
+ if (!anno) {
62
+ if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
63
+ const cell = getEmptyCell(cellTemplate, s, this.dimensions);
64
+ series.cells.push(cell);
65
+ }
66
+ continue;
67
+ }
68
+ const key = anno.key;
69
+ const values = anno.filteredValues || anno.values || [anno.value];
70
+ const numRects = s.cellEncoding == "oncoprint" ? 1 : values.length;
71
+ const height = !s.transpose ? s.rowh / numRects : colw;
72
+ const width = !s.transpose ? colw : colw / values.length;
73
+ const siblingCells = [];
74
+ if (!anno || !anno.renderedValues?.length) {
75
+ if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
76
+ const cell = getEmptyCell(cellTemplate, s, this.dimensions);
77
+ series.cells.push(cell);
78
+ }
79
+ continue;
80
+ }
81
+ for (const [i, value] of values.entries()) {
82
+ const cell = Object.assign({ key, siblingCells }, cellTemplate);
83
+ cell.valueIndex = i;
84
+ let legend;
85
+ if (typeof t.tw.setCellProps == "function") {
86
+ legend = t.tw.setCellProps(cell, anno, value, s, t, this, width, height, dx, dy, i);
87
+ } else {
88
+ const cellProps = t.grp.type == "hierCluster" ? setCellProps["hierCluster"] : t.tw.term.type == "samplelst" ? setCellProps["categorical"] : setCellProps[t.tw.term.type];
89
+ legend = cellProps(cell, t.tw, anno, value, s, t, this, width, height, dx, dy, i);
90
+ }
91
+ if (!s.useCanvas && (cell.x + cell.width < xMin || cell.x - cell.width > xMax)) continue;
92
+ if (legend) {
93
+ for (const l of [legendGroups, so.grp.legendGroups]) {
94
+ if (!l) continue;
95
+ if (!l[legend.group]) {
96
+ l[legend.group] = {
97
+ ref: legend.ref,
98
+ values: {},
99
+ order: legend.order,
100
+ $id,
101
+ origin: legend.entry.origin
102
+ };
103
+ if (legend.entry.dt) l[legend.group].dt = [legend.entry.dt];
104
+ }
105
+ const lg = l[legend.group];
106
+ if (lg.dt && !lg.dt.includes(legend.entry.dt)) lg.dt.push(legend.entry.dt);
107
+ const legendK = legend.entry.origin ? legend.entry.origin + legend.value : legend.value;
108
+ if (!lg.values[legendK]) {
109
+ lg.values[legendK] = JSON.parse(JSON.stringify(legend.entry));
110
+ if (legend.entry.scale) lg.values[legendK].scale = legend.entry.scale;
111
+ }
112
+ if (!lg.values[legendK].samples) lg.values[legendK].samples = /* @__PURE__ */ new Set();
113
+ if (t.tw.term.name === TermTypeGroups.MUTATION_SIGNATURE) {
114
+ if (value?.value > 0) lg.values[legendK].samples.add(row.sample);
115
+ } else lg.values[legendK].samples.add(row.sample);
116
+ if (isDivideByTerm) {
117
+ lg.values[legend.value].isExcluded = so.grp.isExcluded;
118
+ }
119
+ }
120
+ }
121
+ if (!so.grp.isExcluded) {
122
+ if (anno.renderedValues.includes(value)) series.cells.push(cell);
123
+ siblingCells.push(cell);
124
+ }
125
+ }
126
+ if (s.showGrid == "rect" && !so.grp.isExcluded) {
127
+ const cell = t.grp.type == "hierCluster" ? getEmptyCell(cellTemplate, s, this.dimensions) : maySetEmptyCell[t.tw.term.type]?.(siblingCells, cellTemplate, s, this.dimensions);
128
+ if (cell) emptyGridCells.push(cell);
129
+ }
130
+ }
131
+ if (emptyGridCells.length) series.cells.unshift(...emptyGridCells);
132
+ if (series.cells.length) serieses.push(series);
133
+ }
134
+ addAllHiddenLegendGroups(legendGroups, this);
135
+ this.legendData = this.getLegendData(legendGroups, data.refs, this);
136
+ for (const grp of this.sampleGroups) {
137
+ grp.legendData = this.getLegendData(grp.legendGroups, data.refs, this);
138
+ }
139
+ return serieses;
140
+ }
141
+ function addAllHiddenLegendGroups(legendGroups, self) {
142
+ for (const valueFilter of self.config.legendValueFilter.lst) {
143
+ if (valueFilter.tvs.term.type == "categorical" && !legendGroups[valueFilter.tvs.term.$id]) {
144
+ legendGroups[valueFilter.tvs.term.$id] = {
145
+ ref: {},
146
+ values: {},
147
+ $id: valueFilter.tvs.term.$id
148
+ };
149
+ } else if (valueFilter.tvs.term.type == "geneVariant" && !legendGroups[valueFilter.legendGrpName]) {
150
+ legendGroups[valueFilter.legendGrpName] = {
151
+ ref: {},
152
+ values: {},
153
+ dt: [valueFilter.tvs.values[0].dt],
154
+ origin: valueFilter.tvs.values[0].origin
155
+ };
156
+ } else if ((valueFilter.tvs.term.type == "integer" || valueFilter.tvs.term.type == "float") && !legendGroups[valueFilter.tvs.term.$id]) {
157
+ legendGroups[valueFilter.tvs.term.$id] = {
158
+ ref: {},
159
+ values: {},
160
+ $id: valueFilter.tvs.term.$id
161
+ };
162
+ }
163
+ }
164
+ }
165
+
166
+ export {
167
+ getSerieses,
168
+ matrix_serieses_exports
169
+ };
170
+ //# sourceMappingURL=chunk-A2UFOQ3B.js.map