@sjcrh/proteinpaint-client 2.226.0 → 2.227.0

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 (948) hide show
  1. package/dist/2dmaf-B34EJADN.js +1362 -0
  2. package/dist/AggMatrixInput-USCXGZT2.js +402 -0
  3. package/dist/AggregateMatrix-VLCSBD65.js +37 -0
  4. package/dist/AppHeader-KE7QVEW5.js +826 -0
  5. package/dist/BoxPlot-3H5QKYRD.js +1247 -0
  6. package/dist/CorrelationVolcano-ACEJOJS6.js +613 -0
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  8. package/dist/Cuminc-6LPS4LR7.js +1217 -0
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  24. package/dist/NumBinaryEditor-SEC2NDGG.js +274 -0
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  843. /package/dist/{matrix.cells-45ZFADK5.js.map → matrix.cells-A5E63KDN.js.map} +0 -0
  844. /package/dist/{matrix.config-QTBIRXKU.js.map → matrix.config-VLRMO7J2.js.map} +0 -0
  845. /package/dist/{matrix.data-WAMOLSKW.js.map → matrix.data-R4FW2PQH.js.map} +0 -0
  846. /package/dist/{matrix.groups-RXFXZABD.js.map → matrix.groups-3UH2KOIY.js.map} +0 -0
  847. /package/dist/{matrix.integration.spec-JZDZRVOK.js.map → matrix.integration.spec-57YYARQU.js.map} +0 -0
  848. /package/dist/{matrix.interactivity-P4VYGTB2.js.map → matrix.interactivity-KNRJSSTQ.js.map} +0 -0
  849. /package/dist/{matrix.layout-WWPRXXHX.js.map → matrix.layout-OMNDDITA.js.map} +0 -0
  850. /package/dist/{matrix.legend-4MCMVVKO.js.map → matrix.legend-SE7SQTNN.js.map} +0 -0
  851. /package/dist/{matrix.renderers-JQTUODDS.js.map → matrix.renderers-6MMW7XMU.js.map} +0 -0
  852. /package/dist/{matrix.serieses-3IDRKSGO.js.map → matrix.serieses-BEZCQDLJ.js.map} +0 -0
  853. /package/dist/{matrix.sort-EAWOB56R.js.map → matrix.sort-KRNS4VPF.js.map} +0 -0
  854. /package/dist/{matrix.sort.unit.spec-FOWLULHA.js.map → matrix.sort.unit.spec-UXTQPKVV.js.map} +0 -0
  855. /package/dist/{matrix.sorterUi.unit.spec-U5CQDTMX.js.map → matrix.sorterUi.unit.spec-LJJ7GCEB.js.map} +0 -0
  856. /package/dist/{matrix.unit.spec-VTLD4EOZ.js.map → matrix.unit.spec-2OSFPN5T.js.map} +0 -0
  857. /package/dist/{mavb-JIIXJHBK.js.map → mavb-CZAZO6AO.js.map} +0 -0
  858. /package/dist/{mds.samplescatterplot-PTWA2V6E.js.map → mds.samplescatterplot-ENSEO2VX.js.map} +0 -0
  859. /package/dist/{mds.survivalplot-XVZ66GP5.js.map → mds.survivalplot-QSKD6FSX.js.map} +0 -0
  860. /package/dist/{multivalue-2H7QX7MG.js.map → multivalue-FZTFADA2.js.map} +0 -0
  861. /package/dist/{numericDictTermCluster-EHCDRT6J.js.map → numericDictTermCluster-IFIEM3E4.js.map} +0 -0
  862. /package/dist/{oncomatrix-RZLZUC32.js.map → oncomatrix-GZKCAMSR.js.map} +0 -0
  863. /package/dist/{oncomatrix.spec-Z5UQGTW2.js.map → oncomatrix.spec-FTLMVGTH.js.map} +0 -0
  864. /package/dist/{plot.2dvaf-IRBZBJ6B.js.map → plot.2dvaf-PWO4XOFU.js.map} +0 -0
  865. /package/dist/{plot.app-I23IAZ3Z.js.map → plot.app-JYBZEBHK.js.map} +0 -0
  866. /package/dist/{plot.barplot-PYLRAZB7.js.map → plot.barplot-PA2PDVOB.js.map} +0 -0
  867. /package/dist/{plot.boxplot-VBWU7DUG.js.map → plot.boxplot-IHIEWQWG.js.map} +0 -0
  868. /package/dist/{plot.brainImaging-HDJMEMTK.js.map → plot.brainImaging-WQ2WWEW3.js.map} +0 -0
  869. /package/dist/{plot.disco-5BVG3WMT.js.map → plot.disco-QIURLAHA.js.map} +0 -0
  870. /package/dist/{plot.ssgq-S3BKXJMW.js.map → plot.ssgq-T27XDC4K.js.map} +0 -0
  871. /package/dist/{plot.vaf2cov-VD7DU2XR.js.map → plot.vaf2cov-Y2DJRQED.js.map} +0 -0
  872. /package/dist/{polar2-PYLEVG7E.js.map → polar2-3MFBRZ4G.js.map} +0 -0
  873. /package/dist/{profileForms-CI2YYD3Y.js.map → profileForms-J3O7XDHY.js.map} +0 -0
  874. /package/dist/{profilePlot-UCC4ZVHQ.js.map → profilePlot-C45ERAOZ.js.map} +0 -0
  875. /package/dist/{proteomeCohortCompare-2VUSLC6I.js.map → proteomeCohortCompare-2IS7GNJZ.js.map} +0 -0
  876. /package/dist/{pseudbulk.unit.spec-VPZWNTIA.js.map → pseudbulk.unit.spec-SY3ATAPK.js.map} +0 -0
  877. /package/dist/{pseudobulk-RUXGZ7OY.js.map → pseudobulk-N6WNHKAC.js.map} +0 -0
  878. /package/dist/{qualitative-3AVR4GRX.js.map → qualitative-SKUTWJLA.js.map} +0 -0
  879. /package/dist/{qualitative-5QNBKDOZ.js.map → qualitative-XWN5V3EE.js.map} +0 -0
  880. /package/dist/{radar2-AOYMS54Y.js.map → radar2-AHZME5CF.js.map} +0 -0
  881. /package/dist/{radarFacility2-PP2MAXIP.js.map → radarFacility2-CVEVC4U5.js.map} +0 -0
  882. /package/dist/{render-ASLVKYEX.js.map → render-S47OJIIP.js.map} +0 -0
  883. /package/dist/{report-UVYKDMQC.js.map → report-IPX3PKSW.js.map} +0 -0
  884. /package/dist/{sampleView-6UHR7FSR.js.map → sampleView-OZQUKPVV.js.map} +0 -0
  885. /package/dist/{samplelst-ABC2CCNN.js.map → samplelst-7XXJTJ4J.js.map} +0 -0
  886. /package/dist/{samplematrix-36UCHZLC.js.map → samplematrix-JN35HJBG.js.map} +0 -0
  887. /package/dist/{sc-XLSAM725.js.map → sc-6ZHDNPYP.js.map} +0 -0
  888. /package/dist/{scatter-ADOBAOW2.js.map → scatter-4MP6TG67.js.map} +0 -0
  889. /package/dist/{scatter-ZNVLI627.js.map → scatter-TRMY47CC.js.map} +0 -0
  890. /package/dist/{selectGenomeWithTklst-DPDBDYTR.js.map → selectGenomeWithTklst-UDNTL544.js.map} +0 -0
  891. /package/dist/{singleCellCellType-STVPYZD4.js.map → singleCellCellType-UXABRPQQ.js.map} +0 -0
  892. /package/dist/{singleCellCellType.unit.spec-ZLY37AXL.js.map → singleCellCellType.unit.spec-N22EQMZW.js.map} +0 -0
  893. /package/dist/{singleCellGeneExpression-PCGLU35S.js.map → singleCellGeneExpression-OBPVP6IU.js.map} +0 -0
  894. /package/dist/{singleCellGeneExpression.unit.spec-PSLKK362.js.map → singleCellGeneExpression.unit.spec-NVCFU5B4.js.map} +0 -0
  895. /package/dist/{singleCellNumericValue-SR3SJEOB.js.map → singleCellNumericValue-Z2X3LLRB.js.map} +0 -0
  896. /package/dist/{singleCellNumericValue.unit.spec-PXVXJ4HJ.js.map → singleCellNumericValue.unit.spec-Q7DCQHEE.js.map} +0 -0
  897. /package/dist/{singleCellPlot-JXB7M6OH.js.map → singleCellPlot-S5N6ZEEA.js.map} +0 -0
  898. /package/dist/{singlecell-EDSX56QO.js.map → singlecell-OK2P4AS2.js.map} +0 -0
  899. /package/dist/{singlecell-PH55NFRX.js.map → singlecell-RI6HA3NI.js.map} +0 -0
  900. /package/dist/{snp-3VEYBTAQ.js.map → snp-XRM2UAEJ.js.map} +0 -0
  901. /package/dist/{snp.unit.spec-V7OB44US.js.map → snp.unit.spec-CDTYGH4K.js.map} +0 -0
  902. /package/dist/{snplocus-HX67RBT5.js.map → snplocus-CAUGDRZE.js.map} +0 -0
  903. /package/dist/{snplst-H5YXCY33.js.map → snplst-DP533FL2.js.map} +0 -0
  904. /package/dist/{spliceevent.a53ss.diagram-DBDEEHSK.js.map → spliceevent.a53ss.diagram-XWEN4UMO.js.map} +0 -0
  905. /package/dist/{spliceevent.exonskip.diagram-EYEL6BY6.js.map → spliceevent.exonskip.diagram-HBXQOUT4.js.map} +0 -0
  906. /package/dist/{spliceevent.noeventdiagram-64OEXK7U.js.map → spliceevent.noeventdiagram-ORQJ62ON.js.map} +0 -0
  907. /package/dist/{ssGSEA-3YWQH6KM.js.map → ssGSEA-PLDZ2556.js.map} +0 -0
  908. /package/dist/{ssGSEA.unit.spec-23V2IXP5.js.map → ssGSEA.unit.spec-ORFJFZJY.js.map} +0 -0
  909. /package/dist/{stattable-GPSBCNYC.js.map → stattable-GVRVRO2Y.js.map} +0 -0
  910. /package/dist/{studyCatalog-W5PATRNY.js.map → studyCatalog-K46WJHC6.js.map} +0 -0
  911. /package/dist/{summarizeCnvGeneexp-YGI23QH5.js.map → summarizeCnvGeneexp-7WSJTWKH.js.map} +0 -0
  912. /package/dist/{summarizeGeneexpSurvival-KQ6OLWYR.js.map → summarizeGeneexpSurvival-H3TW7I4I.js.map} +0 -0
  913. /package/dist/{summarizeMutationCnv-XDHBNEPU.js.map → summarizeMutationCnv-JOYXEMFP.js.map} +0 -0
  914. /package/dist/{summarizeMutationDiagnosis-VKIJRJ2Q.js.map → summarizeMutationDiagnosis-GBIGXFY5.js.map} +0 -0
  915. /package/dist/{summarizeMutationSurvival-57YKJGLE.js.map → summarizeMutationSurvival-3RULG3KW.js.map} +0 -0
  916. /package/dist/{summary-4WQOVIUF.js.map → summary-VKLFTPC2.js.map} +0 -0
  917. /package/dist/{summary.integration.spec-FRNWBU7F.js.map → summary.integration.spec-EK3MPFVD.js.map} +0 -0
  918. /package/dist/{summaryInput-X7DS2YA7.js.map → summaryInput-POI5KQSP.js.map} +0 -0
  919. /package/dist/{sunburst-MSGTXYMM.js.map → sunburst-BIVYHF5R.js.map} +0 -0
  920. /package/dist/{sunburst-3OEAQA3O.js.map → sunburst-SYHQOCGQ.js.map} +0 -0
  921. /package/dist/{survival-5KC5CNZU.js.map → survival-CG2GQ4YY.js.map} +0 -0
  922. /package/dist/{survival-QXDS6N46.js.map → survival-NEO3E2HS.js.map} +0 -0
  923. /package/dist/{survival.integration.spec-PKENHLTZ.js.map → survival.integration.spec-PPK5KO4V.js.map} +0 -0
  924. /package/dist/{svgraph-VJLB7BBN.js.map → svgraph-Q2U2HEMF.js.map} +0 -0
  925. /package/dist/{swimmer-R3DN7N36.js.map → swimmer-GA4C6YH7.js.map} +0 -0
  926. /package/dist/{table-YF5VORU6.js.map → table-DJJIES6L.js.map} +0 -0
  927. /package/dist/{termCollection-KSHVOPS5.js.map → termCollection-CHVUM5C6.js.map} +0 -0
  928. /package/dist/{termCollection-3KGLZFDW.js.map → termCollection-R3LTBPJ4.js.map} +0 -0
  929. /package/dist/{termCollection.unit.spec-HTBDG5PL.js.map → termCollection.unit.spec-B7KAAOFT.js.map} +0 -0
  930. /package/dist/{termCollectionFractionSelection-MK4NKWUX.js.map → termCollectionFractionSelection-A72QM36J.js.map} +0 -0
  931. /package/dist/{termCollectionFractionSelection.unit.spec-AMF32FDN.js.map → termCollectionFractionSelection.unit.spec-JR77QEIG.js.map} +0 -0
  932. /package/dist/{tk-Z54DOECH.js.map → tk-GRGKFATN.js.map} +0 -0
  933. /package/dist/{tp.ui-M4TZVT53.js.map → tp.ui-NATRJ5EN.js.map} +0 -0
  934. /package/dist/{tvs.categorical-HY3BWCZR.js.map → tvs.categorical-U2ZYLPSW.js.map} +0 -0
  935. /package/dist/{tvs.condition-Y36TRIX4.js.map → tvs.condition-6EBZALR4.js.map} +0 -0
  936. /package/dist/{tvs.dt-XKVJZP7Y.js.map → tvs.dt-H626ESMQ.js.map} +0 -0
  937. /package/dist/{tvs.dtcnv.categorical-OMRZR4Y7.js.map → tvs.dtcnv.categorical-6S7INDYC.js.map} +0 -0
  938. /package/dist/{tvs.dtcnv.continuous-AGYOBI5K.js.map → tvs.dtcnv.continuous-MLYNEMHI.js.map} +0 -0
  939. /package/dist/{tvs.dtfusion-2JX5Y2IH.js.map → tvs.dtfusion-2OLY6X7G.js.map} +0 -0
  940. /package/dist/{tvs.dtitd-SDSLBBWC.js.map → tvs.dtitd-Z6MEL5SH.js.map} +0 -0
  941. /package/dist/{tvs.dtsnvindel-LI7K464K.js.map → tvs.dtsnvindel-HPBQSCYV.js.map} +0 -0
  942. /package/dist/{tvs.dtsv-VRCLX7QY.js.map → tvs.dtsv-BRRNX64J.js.map} +0 -0
  943. /package/dist/{tvs.multivalue-4OTY6J2S.js.map → tvs.multivalue-H2G7WKAL.js.map} +0 -0
  944. /package/dist/{tvs.numeric-CDATYOR2.js.map → tvs.numeric-OKYGMQSK.js.map} +0 -0
  945. /package/dist/{tvs.samplelst-76JOJG2M.js.map → tvs.samplelst-46FGACU7.js.map} +0 -0
  946. /package/dist/{tvs.survival-WTFJOKIZ.js.map → tvs.survival-QL4KC3SQ.js.map} +0 -0
  947. /package/dist/{tvs.termCollection-QQXAS7PE.js.map → tvs.termCollection-22DFW3PF.js.map} +0 -0
  948. /package/dist/{vocabulary-6ACAEFTL.js.map → vocabulary-LJEERZJ6.js.map} +0 -0
@@ -1,1247 +0,0 @@
1
- import {
2
- getDefaultBoxplotSettings
3
- } from "./chunk-GZL6YFZJ.js";
4
- import {
5
- CustomDownloadMenu,
6
- ListSamples,
7
- PlotBase,
8
- axisstyle,
9
- controlsInit,
10
- defaultUiLabels,
11
- descrStatsToTSV,
12
- drawBoxplot,
13
- fillTermWrapper,
14
- getChartTitle,
15
- getCombinedTermFilter,
16
- getMaxLabelWidth,
17
- getSingleCellSpecialCase,
18
- getT0T2defaultQ,
19
- joinToFilterUiRoot,
20
- renderTable,
21
- renderTerm1Label,
22
- setDescrStatsByTerm,
23
- testRowsToTSV
24
- } from "./chunk-DPWSIN62.js";
25
- import "./chunk-HJ6L54YS.js";
26
- import "./chunk-KZ54E2FU.js";
27
- import {
28
- Menu
29
- } from "./chunk-CNFTQSNE.js";
30
- import "./chunk-DOC3HBOV.js";
31
- import "./chunk-TVJOSRCH.js";
32
- import "./chunk-3CIL7KH7.js";
33
- import "./chunk-T4XPCSLP.js";
34
- import {
35
- pairwiseTestGroupsLimit
36
- } from "./chunk-6V7ITU5F.js";
37
- import "./chunk-W5J3LTYS.js";
38
- import "./chunk-KUOXZIH4.js";
39
- import {
40
- isNumTermCollection,
41
- isNumericTerm
42
- } from "./chunk-T2W4JHWJ.js";
43
- import {
44
- axisLeft,
45
- axisTop,
46
- isErrorResponse
47
- } from "./chunk-2N345NXD.js";
48
- import {
49
- copyMerge,
50
- getCompInit
51
- } from "./chunk-HBNB5TRH.js";
52
- import "./chunk-PF4DSFDR.js";
53
- import {
54
- format,
55
- linear,
56
- log
57
- } from "./chunk-4OLM3KSB.js";
58
- import "./chunk-PWYMHUXY.js";
59
- import {
60
- decimalPlacesUntilFirstNonZero
61
- } from "./chunk-TLT4YIG3.js";
62
- import "./chunk-5R63Q5KH.js";
63
- import {
64
- select_default
65
- } from "./chunk-I6Y4O3RR.js";
66
- import {
67
- rgb
68
- } from "./chunk-Q5RDQNIT.js";
69
- import "./chunk-HS5PO5ZQ.js";
70
-
71
- // plots/boxplot/model/Model.ts
72
- var Model = class {
73
- constructor(boxplot, config) {
74
- this.boxplot = boxplot;
75
- this.config = config;
76
- this.state = boxplot.state;
77
- this.app = boxplot.app;
78
- this.settings = config.settings.boxplot;
79
- }
80
- async getData() {
81
- const data = await this.app.vocabApi.getViolinBox(
82
- this.setRequestOpts(),
83
- {},
84
- this.boxplot.api?.getAbortSignal()
85
- );
86
- return data;
87
- }
88
- setRequestOpts() {
89
- const isNumericTC = this.config.term.term.type == "termCollection" && this.config.term.term.memberType == "numeric";
90
- const opts = {
91
- plotType: "box",
92
- tw: this.getContinousTerm(),
93
- filter: this.state.termfilter.filter,
94
- filter0: this.state.termfilter.filter0,
95
- orderByMedian: this.settings.orderByMedian,
96
- isLogScale: this.settings.isLogScale,
97
- removeOutliers: this.settings.removeOutliers,
98
- showAssocTests: this.settings.showAssocTests,
99
- maxPairwiseTestGroups: this.settings.maxPairwiseTestGroups
100
- };
101
- if (!isNumericTC) {
102
- if (this.config.term2)
103
- opts.overlayTw = this.getContinousTerm() == this.config.term ? this.config.term2 : this.config.term;
104
- if (this.config.term0) opts.divideTw = this.config.term0;
105
- }
106
- return opts;
107
- }
108
- getContinousTerm() {
109
- if (!this.config?.term2) return this.config.term;
110
- if (this.config.term.term.type == "termCollection" && this.config.term.term.memberType == "numeric")
111
- return this.config.term;
112
- return isNumericTerm(this.config.term.term) && this.config.term.q.mode == "continuous" ? this.config.term : this.config.term2;
113
- }
114
- };
115
-
116
- // plots/boxplot/viewModel/LegendDataMapper.ts
117
- var LegendDataMapper = class {
118
- constructor(config) {
119
- this.legendData = [];
120
- this.config = config;
121
- const isTerm2 = config?.term2;
122
- if (config.term.term.type != "termCollection" && config.term.q?.descrStats) {
123
- this.legendData.push({
124
- label: `Descriptive Statistics${isTerm2 ? `: ${config.term.term.name}` : ""}`,
125
- items: this.setDescrStatItems(config.term.q.descrStats)
126
- });
127
- }
128
- if (isTerm2 && isTerm2.q?.descrStats) {
129
- this.legendData.push({
130
- label: `Descriptive Statistics: ${config.term2.term.name}`,
131
- items: this.setDescrStatItems(isTerm2.q.descrStats)
132
- });
133
- }
134
- }
135
- map(charts, uncomputableValues) {
136
- const hiddenPlots = this.getHiddenPlots(charts);
137
- if (this.config.term.term?.values) {
138
- const term1Label = this.config.term2 ? this.config.term.term.name : "Other categories";
139
- const term1Data = this.setHiddenCategoryItems(this.config.term, term1Label, hiddenPlots, uncomputableValues || []);
140
- if (term1Data) this.legendData.push(term1Data);
141
- }
142
- if (this.config.term2?.term?.values) {
143
- const term2Data = this.setHiddenCategoryItems(
144
- this.config.term2,
145
- this.config.term2.term.name,
146
- hiddenPlots,
147
- uncomputableValues || []
148
- );
149
- if (term2Data) this.legendData.push(term2Data);
150
- }
151
- return this.legendData;
152
- }
153
- getHiddenPlots(charts) {
154
- const hiddenPlots = Object.values(charts).reduce((plotMap, chart) => {
155
- for (const p of chart.plots ?? []) {
156
- if (!p.isHidden || plotMap.has(p.key)) continue;
157
- plotMap.set(p.key, {
158
- key: p.key,
159
- text: p.key,
160
- isHidden: true,
161
- isPlot: true
162
- });
163
- }
164
- return plotMap;
165
- }, /* @__PURE__ */ new Map()).values();
166
- return Array.from(hiddenPlots);
167
- }
168
- setDescrStatItems(stats) {
169
- return Object.values(stats).map((s) => ({
170
- key: s.key,
171
- text: `${s.label}: ${s.value}`,
172
- isHidden: false,
173
- isPlot: false
174
- }));
175
- }
176
- setHiddenCategoryItems(tw, label, hiddenPlots, uncomputableValues) {
177
- const termData = { label, items: [] };
178
- if (hiddenPlots.length) {
179
- for (const key of Object.keys(tw.q.hiddenValues || {})) {
180
- const plot = hiddenPlots.find((p) => p.key === key);
181
- if (plot) termData.items.push(plot);
182
- }
183
- }
184
- if (uncomputableValues && uncomputableValues.length) {
185
- for (const v of Object.values(tw.term.values || {})) {
186
- const uncomputableItem = uncomputableValues.find((u) => u.label === v.label);
187
- if (uncomputableItem) {
188
- termData.items.push({
189
- key: uncomputableItem.label,
190
- text: `${uncomputableItem.label}, n=${uncomputableItem.value}`,
191
- isHidden: true,
192
- isPlot: false
193
- });
194
- }
195
- }
196
- }
197
- return termData.items.length ? termData : null;
198
- }
199
- };
200
-
201
- // plots/boxplot/viewModel/ChartsDataMapper.ts
202
- var ChartsDataMapper = class {
203
- /** Top padding for the svg */
204
- #topPad = 20;
205
- /** Bottom padding for the svg */
206
- #bottomPad = 25;
207
- /** Horizontal, or right and left padding */
208
- #horizPad = 120;
209
- /** For outliers, set a radius rather than using the default. */
210
- #outRadius = 5;
211
- /** Offset applied when divide by term is present
212
- * Creates space for the subtitle*/
213
- #divideByOffset = 20;
214
- constructor(data, settings, maxLabelLgth, useDefaultSettings) {
215
- this.validateInputData(data);
216
- this.absMin = data.absMin;
217
- this.absMax = data.absMax;
218
- this.charts = Object.values(data.charts);
219
- this.settings = settings;
220
- if (useDefaultSettings) {
221
- const { rowHeight, rowSpace } = this.getRowSettings(this.charts);
222
- this.rowHeight = rowHeight;
223
- this.rowSpace = rowSpace;
224
- } else {
225
- this.rowHeight = settings.rowHeight;
226
- this.rowSpace = settings.rowSpace;
227
- }
228
- this.totalLabelSize = maxLabelLgth + settings.labelPad;
229
- this.totalBoxSize = this.rowHeight + this.rowSpace;
230
- }
231
- /** Same checks are in the server route */
232
- validateInputData(data) {
233
- if (!data) throw new Error("No data provided to ChartDataMapper");
234
- if (!data.charts) throw new Error("No charts data provided to ChartDataMapper");
235
- if (!Array.isArray(data.charts) && typeof data.charts !== "object")
236
- throw new Error("Invalid charts data provided to ChartDataMapper");
237
- if (data.absMin === void 0 || data.absMax === void 0)
238
- throw new Error("Missing absMin or absMax in data provided to ChartDataMapper");
239
- }
240
- /** Set the row settings based on all plots */
241
- getRowSettings(charts) {
242
- let totalNumPlots = 0;
243
- for (const chart of charts) {
244
- totalNumPlots = totalNumPlots + chart.plots.filter((p) => !p.isHidden).length;
245
- }
246
- const isLargePlotCount = totalNumPlots > 20;
247
- const rowHeight = totalNumPlots > 10 ? isLargePlotCount ? 20 : 35 : 50;
248
- const rowSpace = totalNumPlots > 10 ? isLargePlotCount ? 10 : 12 : 15;
249
- return { rowHeight, rowSpace };
250
- }
251
- map(config) {
252
- const chartData = {};
253
- for (const chart of this.charts) {
254
- let incrPad = 40;
255
- const plotDim = this.setPlotDimensions(chart, config, this.settings, incrPad);
256
- if (config?.term0) incrPad += this.#divideByOffset;
257
- incrPad += 30;
258
- chartData[chart.chartId] = {
259
- plotDim,
260
- plots: this.setPlotData(chart, config, this.settings, incrPad),
261
- wilcoxon: chart?.wilcoxon || null,
262
- pairwiseTestMessage: chart?.pairwiseTestMessage
263
- };
264
- }
265
- return chartData;
266
- }
267
- setPlotDimensions(chart, config, settings, incrPad) {
268
- const svg = this.setSvgDimensions(settings, chart, incrPad, config);
269
- const plotCenter = this.totalLabelSize + settings.plotLength / 2;
270
- const plotDim = {
271
- //Add 1 to the max is big enough so the upper line to boxplot isn't cutoff
272
- domain: [this.absMin, this.absMax <= 1 ? this.absMax : this.absMax + 1],
273
- range: [0, settings.plotLength],
274
- svg,
275
- subtitle: this.setSubtitleDimensions(
276
- config,
277
- settings,
278
- svg.height,
279
- chart.chartId,
280
- chart.sampleCount,
281
- plotCenter,
282
- incrPad
283
- ),
284
- title: this.setTitleDimensions(config, settings, svg.height, plotCenter, incrPad),
285
- axis: {
286
- x: settings.isVertical ? this.#horizPad / 2 + incrPad + this.#topPad : this.totalLabelSize,
287
- y: this.#topPad + (settings.isVertical ? settings.labelPad : incrPad + 20),
288
- values: (ticks) => {
289
- if (settings.isLogScale) return this.filterTickValues(ticks);
290
- return ticks;
291
- },
292
- format: (d) => {
293
- if (settings.isLogScale) {
294
- if (Number.isInteger(d)) return format(".0f")(d);
295
- const dec = decimalPlacesUntilFirstNonZero(d);
296
- if (dec > 1) return format(`.${dec + 1}f`)(d);
297
- return format(".2f")(d);
298
- }
299
- return d.toString();
300
- }
301
- }
302
- };
303
- if (config?.term0) {
304
- if (settings.isVertical) plotDim.axis.x += this.#divideByOffset;
305
- else plotDim.axis.y += this.#divideByOffset;
306
- }
307
- return plotDim;
308
- }
309
- setSvgDimensions(settings, chart, incrPad, config) {
310
- let plotsSpace = chart.plots.filter((p) => !p.isHidden).length * this.totalBoxSize + this.#topPad + this.#bottomPad + incrPad;
311
- if (config?.term0) plotsSpace += this.#divideByOffset + incrPad;
312
- const length = settings.plotLength + this.totalLabelSize + this.#horizPad / 2;
313
- return {
314
- width: settings.isVertical ? plotsSpace + this.#horizPad : length,
315
- height: settings.isVertical ? length : plotsSpace
316
- };
317
- }
318
- setSubtitleDimensions(config, settings, height, chartId, sampleCount, plotCenter, incrPad) {
319
- const dim = {
320
- x: null,
321
- y: null,
322
- text: null
323
- };
324
- if (config.term0) {
325
- dim.x = settings.isVertical ? this.#horizPad / 2 : plotCenter;
326
- dim.y = settings.isVertical ? height - plotCenter - this.#horizPad / 2 : this.#topPad + incrPad / 2;
327
- dim.text = getChartTitle(config, chartId, sampleCount);
328
- }
329
- return dim;
330
- }
331
- setTitleDimensions(config, settings, height, plotCenter, incrPad) {
332
- const dim = {
333
- x: settings.isVertical ? this.#horizPad / 2 : plotCenter,
334
- y: settings.isVertical ? height - plotCenter - this.#horizPad / 2 : this.#topPad + incrPad / 2,
335
- text: config.term.q.mode == "continuous" ? config.term.term.name : config.term2.term.name
336
- };
337
- if (config?.term0) {
338
- if (settings.isVertical) dim.x += this.#divideByOffset + 10;
339
- else dim.y += this.#divideByOffset + 10;
340
- }
341
- return dim;
342
- }
343
- filterTickValues(ticks) {
344
- if (!ticks || ticks.length == 0) {
345
- throw new Error("No ticks provided to filterTickValues");
346
- }
347
- const significantLessThanOne = ticks.filter((t) => t < 1).length / ticks.length;
348
- const range = ticks[ticks.length - 1] - ticks[0];
349
- const spread = range > 1e3 ? 4 : range > 100 ? 3 : 2;
350
- const formattedTicks = ticks.filter((t, i) => {
351
- if (t === 0 || i == ticks.length - 1 && i % spread !== 0) return t;
352
- else if (t <= 1 && significantLessThanOne > 0.5) {
353
- if (i % 5 === 0) return t;
354
- } else if (i % spread === 0) return t;
355
- });
356
- return formattedTicks;
357
- }
358
- setPlotData(chart, config, settings, incrPad) {
359
- const plots = structuredClone(chart.plots.filter((p) => !p.isHidden));
360
- for (const plot of plots) {
361
- let color;
362
- const term2 = config.term2;
363
- if (term2) {
364
- if (term2.q.type == "predefined-groupset" || term2.q.type == "custom-groupset") {
365
- const groupset = term2.q.type == "predefined-groupset" ? term2.term.groupsetting.lst[term2.q.predefined_groupset_idx] : term2.q.customset;
366
- if (!groupset) throw "groupset is missing";
367
- const group = groupset.groups.find((g) => g.name == plot.seriesId);
368
- if (group?.color) color = group.color;
369
- } else {
370
- color = term2.term.values?.[plot.seriesId]?.color;
371
- }
372
- }
373
- if (!color) color = settings.color;
374
- if (!plot.color) plot.color = color;
375
- if (settings.displayMode == "dark") plot.color = rgb(plot.color).brighter(0.75);
376
- if (plot.boxplot.out.length) {
377
- const maxOut = plot.boxplot.out.reduce(
378
- (a, b) => Math.max(a.value, b.value)
379
- );
380
- if (maxOut && maxOut.value > chart.absMax) chart.absMax = maxOut.value;
381
- plot.boxplot.radius = this.#outRadius;
382
- }
383
- plot.boxplot.rectFill = settings.displayMode == "dark" ? "black" : settings.displayMode == "filled" ? color : "white";
384
- plot.x = settings.isVertical ? this.#horizPad / 2 + incrPad : this.totalLabelSize;
385
- plot.y = this.#topPad + (settings.isVertical ? settings.plotLength + settings.labelPad : incrPad);
386
- incrPad += this.totalBoxSize;
387
- plot.chartId = chart.chartId || " ";
388
- }
389
- return plots;
390
- }
391
- };
392
-
393
- // plots/boxplot/viewModel/ViewModel.ts
394
- var ViewModel = class {
395
- constructor(config, data, settings, maxLabelLgth, useDefaultSettings) {
396
- const chartsMapper = new ChartsDataMapper(data, settings, maxLabelLgth, useDefaultSettings);
397
- const legendMapper = new LegendDataMapper(config);
398
- const charts = chartsMapper.map(config);
399
- this.rowHeight = chartsMapper.rowHeight;
400
- this.rowSpace = chartsMapper.rowSpace;
401
- this.viewData = {
402
- backgroundColor: settings.displayMode == "dark" ? "black" : "white",
403
- textColor: settings.displayMode == "dark" ? "white" : "black",
404
- charts,
405
- legend: legendMapper.map(data.charts, data.uncomputableValues || [])
406
- };
407
- }
408
- };
409
-
410
- // plots/boxplot/interactions/BoxPlotInteractions.ts
411
- var BoxPlotInteractions = class {
412
- constructor(boxplot, getResData) {
413
- this.app = boxplot.app;
414
- this.boxplot = boxplot;
415
- this.dom = boxplot.dom;
416
- this.id = boxplot.id;
417
- this.getResData = getResData;
418
- }
419
- help() {
420
- window.open("https://github.com/stjude/proteinpaint/wiki/Box-plot");
421
- }
422
- /** Option to add a global filter from the box plot label menu. */
423
- addFilter(plot) {
424
- const sampleList = this.initListSamples(plot);
425
- const filter = joinToFilterUiRoot(this.app.getState().termfilter.filter, [sampleList.tvslst]);
426
- this.app.dispatch({
427
- type: "filter_replace",
428
- filter
429
- });
430
- }
431
- /** Option to hide a plot from the box plot label menu. */
432
- hidePlot(plot) {
433
- const plotConfig = this.getPlotConfig();
434
- const config = structuredClone(plotConfig);
435
- const contTerm = config.term.q.mode == "continuous" ? "term2" : "term";
436
- if (!config[contTerm].q.hiddenValues) config[contTerm].q.hiddenValues = {};
437
- config[contTerm].q.hiddenValues[plot.key] = 1;
438
- this.app.dispatch({
439
- type: "plot_edit",
440
- id: this.id,
441
- config
442
- });
443
- }
444
- /** Trigger when clicking on a hidden plot in the legend */
445
- unhidePlot(item) {
446
- const plotConfig = this.getPlotConfig();
447
- const config = structuredClone(plotConfig);
448
- const contTerm = config.term.q.mode == "continuous" ? "term2" : "term";
449
- delete config[contTerm].q.hiddenValues[item.key];
450
- this.app.dispatch({
451
- type: "plot_edit",
452
- id: this.id,
453
- config
454
- });
455
- }
456
- initListSamples(plot) {
457
- const state = this.app.getState();
458
- const plotConfig = this.getPlotConfig();
459
- const config = structuredClone(plotConfig);
460
- const bins = this.getResData().bins;
461
- const start = this.getResData().absMin;
462
- const end = this.getResData().absMax;
463
- const contTerm = config.term.q.mode == "continuous" ? config.term : config.term2;
464
- const term = config.term != contTerm ? contTerm : config.term;
465
- const term2 = config.term != contTerm ? config.term : config.term2;
466
- const sampleList = new ListSamples({
467
- app: this.app,
468
- termfilter: state.termfilter,
469
- term,
470
- term2,
471
- term0: config.term0,
472
- plot,
473
- bins,
474
- start,
475
- end
476
- });
477
- return sampleList;
478
- }
479
- /** Option from box plot label to show the samples in a table within the tooltip. */
480
- async listSamples(plot) {
481
- const sampleList = this.initListSamples(plot);
482
- const data = await sampleList.getData();
483
- const [rows, columns, samples] = sampleList.setTableData(data);
484
- return [rows, columns, samples];
485
- }
486
- /** Callback for color picker in plot(s) label menu */
487
- updatePlotColor(plot, color) {
488
- if (!plot.seriesId) return;
489
- const plotConfig = this.getPlotConfig();
490
- const config = structuredClone(plotConfig);
491
- config.term2.term.values[plot.seriesId].color = color;
492
- this.app.dispatch({
493
- type: "plot_edit",
494
- id: this.id,
495
- config
496
- });
497
- }
498
- getPlotConfig() {
499
- return this.boxplot.state.config;
500
- }
501
- clearDom() {
502
- this.dom.error.style("padding", "").text("");
503
- this.dom.charts.selectAll("*").remove();
504
- this.dom.legend.selectAll("*").remove();
505
- }
506
- };
507
-
508
- // plots/boxplot/view/LegendRender.ts
509
- var LegendRenderer = class {
510
- constructor(legendDiv, legendData, interactions, textColor) {
511
- this.interactions = interactions;
512
- this.textColor = textColor;
513
- this.renderLegend(legendDiv, legendData);
514
- }
515
- renderLegend(legendDiv, legendData) {
516
- legendDiv.attr("id", "sjpp-boxplot-legend");
517
- for (const section of legendData) {
518
- legendDiv.append("div").style("opacity", "0.75").style("color", this.textColor).text(section.label);
519
- const sectionDiv = legendDiv.append("div").style("padding-left", "10px");
520
- for (const item of section.items) {
521
- this.addItem(item, sectionDiv);
522
- }
523
- }
524
- }
525
- addItem(item, sectionDiv) {
526
- const legendItem = sectionDiv.append("div");
527
- if (item.isPlot) {
528
- legendItem.append("div").style("display", "inline-block").style("margin-right", "3px").style("position", "relative").style("vertical-align", "middle").html(`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="${this.textColor}" class="bi bi-arrow-counterclockwise" viewBox="0 0 16 16" style="vertical-align: middle; display: block; margin: auto;">
529
- <path stroke="#000" stroke-width="0.25" fill-rule="evenodd" d="M8 3a5 5 0 1 1-4.546 2.914.5.5 0 0 0-.908-.417A6 6 0 1 0 8 2v1z"/>
530
- <path d="M8 4.466V.534a.25.25 0 0 0-.41-.192L5.23 2.308a.25.25 0 0 0 0 .384l2.36 1.966A.25.25 0 0 0 8 4.466z"/>
531
- </svg>`);
532
- }
533
- legendItem.append("div").style("display", "inline-block").style("color", this.textColor).style("text-decoration", item.isHidden ? "line-through" : "").text(item.text);
534
- if (item.isPlot) {
535
- legendItem.attr("aria-label", `Click to unhide plot`).on("click", () => {
536
- this.interactions.unhidePlot(item);
537
- });
538
- }
539
- }
540
- };
541
-
542
- // plots/boxplot/view/BoxPlotToolTips.ts
543
- var BoxPlotToolTips = class {
544
- constructor(plot, g, tip, isVertical) {
545
- this.tablePadding = "3px";
546
- this.plot = plot;
547
- this.g = g;
548
- this.boxplot = plot.boxplot;
549
- this.isVertical = isVertical;
550
- this.tip = tip;
551
- this.addLabelTooltip();
552
- this.addOutliersTooltip();
553
- }
554
- //Add rendering preferences here to maintain styles
555
- //across all tooltip instances
556
- addText(text) {
557
- this.tip.d.append("div").text(text);
558
- }
559
- addLabelTooltip() {
560
- if (Object.keys(this.plot.descrStats).length < 2) return;
561
- this.boxplot.labelG.on("mouseover", (event) => {
562
- this.tip.clear();
563
- if (this.isVertical) this.tip.show(event.clientX, event.clientY);
564
- else this.tip.showunder(this.boxplot.labelG.node());
565
- const table = this.tip.d.append("table").attr("class", "sja_simpletable");
566
- table.append("tr").style("text-align", "center").append("td").attr("colspan", 2).style("padding", this.tablePadding).text(this.plot.key);
567
- for (const stat of Object.values(this.plot.descrStats)) {
568
- const row = table.append("tr");
569
- row.append("td").style("padding", this.tablePadding).style("opacity", 0.5).text(stat.label);
570
- row.append("td").style("padding", this.tablePadding).style("text-align", "center").style("opacity", stat.value === null || stat.value === void 0 ? 0.5 : 1).text(stat.value ?? "N/A");
571
- }
572
- });
573
- this.boxplot.labelG.on("mouseout", () => {
574
- this.tip.hide();
575
- });
576
- }
577
- // addLineToolTips() {
578
- // const addToolTips = (elem, text: string) => {
579
- // const elemBBox = elem.node().getBBox()
580
- // //Add an expanded area for the tooltip
581
- // //Easier for user to hover over
582
- // this.g
583
- // .append('rect')
584
- // .attr('x', elemBBox.x - 10)
585
- // .attr('y', elemBBox.y - 10)
586
- // .attr('width', elemBBox.width + 20)
587
- // .attr('height', elemBBox.height + 20)
588
- // .attr('fill', 'transparent')
589
- // .style('pointer-events', 'all')
590
- // .on('mouseover', () => {
591
- // this.tip.clear().showunder(elem.node())
592
- // this.addText(text)
593
- // })
594
- // .on('mouseout', () => {
595
- // this.tip.hide()
596
- // })
597
- // }
598
- // if (this.boxplot.linep50) {
599
- // const median = this.plot.descrStats.find((d: any) => d.id == 'median')
600
- // if (!median) throw `Missing median value for ${this.plot.key}`
601
- // addToolTips(this.boxplot.linep50, `Median: ${median.value}`)
602
- // }
603
- // if (this.boxplot.linew1) {
604
- // addToolTips(this.boxplot.linew1, `${this.boxplot.w1}`)
605
- // }
606
- // if (this.boxplot.linew2) {
607
- // addToolTips(this.boxplot.linew2, `${this.boxplot.w2}`)
608
- // }
609
- // }
610
- addOutliersTooltip() {
611
- this.g.selectAll("circle").data(this.boxplot.out).each((d, i, nodes) => {
612
- const circle = select_default(nodes[i]);
613
- circle.on("mouseover", () => {
614
- this.tip.clear().showunder(circle.node());
615
- this.addText(d.value);
616
- });
617
- circle.on("mouseout", () => {
618
- this.tip.hide();
619
- });
620
- });
621
- }
622
- };
623
-
624
- // plots/boxplot/view/BoxPlotLabelMenu.ts
625
- var BoxPlotLabelMenu = class {
626
- constructor(plot, app, interactions, tip, isVertical) {
627
- const options = [];
628
- if (app.getState().nav.header_mode === "with_tabs")
629
- options.push({
630
- text: `Add filter: ${plot.key}`,
631
- isVisible: () => true,
632
- callback: () => interactions.addFilter(plot)
633
- });
634
- options.push({
635
- text: `Hide ${plot.key}`,
636
- isVisible: () => true,
637
- callback: () => interactions.hidePlot(plot)
638
- });
639
- const { samples } = interactions.getPlotConfig().controlLabels;
640
- if (app.getState().nav.header_mode === "with_tabs")
641
- options.push({
642
- text: `List ${samples}`,
643
- isVisible: (state) => state.termdbConfig.displaySampleIds && app.vocabApi.hasVerifiedToken(),
644
- callback: async (event) => {
645
- if (isVertical) tip.clear().show(event.clientX, event.clientY);
646
- else tip.clear().showunder(plot.boxplot.labelG.node());
647
- const [rows, columns] = await interactions.listSamples(plot);
648
- const tableDiv = tip.d.append("div");
649
- renderTable({
650
- rows,
651
- columns,
652
- div: tableDiv,
653
- maxHeight: "35vh",
654
- resize: true,
655
- showLines: true,
656
- dataTestId: "sjpp-listsampletable"
657
- });
658
- }
659
- });
660
- if (app.opts?.boxplot?.allow2selectSamples) {
661
- const ss = app.opts.boxplot.allow2selectSamples;
662
- options.push({
663
- text: ss.buttonText,
664
- isVisible: (state) => state.termdbConfig.displaySampleIds && app.vocabApi.hasVerifiedToken(),
665
- callback: async () => {
666
- const table = await interactions.listSamples(plot);
667
- const samples2 = table[2];
668
- ss.callback({
669
- samples: await app.vocabApi.convertSampleId(samples2, ss.attributes),
670
- source: ss.defaultSelectionLabel || `Selected from boxplot`
671
- });
672
- }
673
- });
674
- }
675
- plot.boxplot.labelG.on("click", (event) => {
676
- tip.clear();
677
- if (isVertical) tip.show(event.clientX, event.clientY);
678
- else tip.showunder(plot.boxplot.labelG.node());
679
- const state = app.getState();
680
- for (const opt of options) {
681
- if (!opt.isVisible(state)) continue;
682
- tip.d.append("div").classed("sja_menuoption", true).text(opt.text).on("click", (event2) => {
683
- tip.hide();
684
- opt.callback(event2);
685
- });
686
- }
687
- if (plot.color) {
688
- tip.d.append("div").style("padding", "5px 10px").style("display", "inline-block").text("Color:").append("input").attr("type", "color").property("value", rgb(plot.color).formatHex()).on("change", (event2) => {
689
- interactions.updatePlotColor(plot, event2.target.value);
690
- tip.hide();
691
- });
692
- }
693
- });
694
- }
695
- };
696
-
697
- // plots/boxplot/view/AssociationTableRender.ts
698
- var AssociationTableRender = class {
699
- constructor(div, data, message) {
700
- const wrapper = div.style("vertical-align", "top").style("margin-top", "30px");
701
- wrapper.append("div").text("Group comparisons (Wilcoxon's rank sum test)").style("font-weight", "600").style("text-align", "center");
702
- const tableDiv = wrapper.append("div").style("margin-top", "5px");
703
- renderTable({
704
- div: tableDiv,
705
- columns: [{ label: "Group 1" }, { label: "Group 2" }, { label: "P-Value" }],
706
- rows: data,
707
- footerRow: message ? { text: message, className: "sja_warnbar" } : void 0
708
- });
709
- }
710
- };
711
-
712
- // plots/boxplot/view/ChartRender.ts
713
- var ChartRender = class {
714
- constructor(dom, settings, app, interactions, chart, backgroundColor, textColor) {
715
- this.app = app;
716
- this.interactions = interactions;
717
- this.textColor = textColor;
718
- const plotDim = chart.plotDim;
719
- dom.svg.transition().attr("width", plotDim.svg.width).attr("height", plotDim.svg.height).style("fill", backgroundColor);
720
- const setScaleFunc = settings.isLogScale ? log().base(10) : linear();
721
- const scale = setScaleFunc.domain(plotDim.domain).range(plotDim.range);
722
- this.renderTitles(plotDim, dom, settings);
723
- this.renderBoxPlots(dom, chart, scale, settings);
724
- this.renderAxis(plotDim, dom, scale, settings);
725
- if (chart.wilcoxon && dom.assocTableDiv) {
726
- new AssociationTableRender(dom.assocTableDiv, chart.wilcoxon, chart.pairwiseTestMessage);
727
- }
728
- }
729
- renderTitles(plotDim, dom, settings) {
730
- const transformStr = `translate(${plotDim.title.x}, ${plotDim.title.y})${settings.isVertical ? `,rotate(-90)` : ""}`;
731
- dom.title.attr("class", "sjpp-boxplot-title").style("font-weight", 600).attr("text-anchor", "middle").attr("transform", transformStr).attr("fill", this.textColor).text(plotDim.title.text.length > 80 ? plotDim.title.text.slice(0, 80) + "..." : plotDim.title.text);
732
- if (plotDim.subtitle.text) {
733
- const subTransformStr = `translate(${plotDim.subtitle.x}, ${plotDim.subtitle.y})${settings.isVertical ? `,rotate(-90)` : ""}`;
734
- dom.subtitle.attr("class", "sjpp-boxplot-subtitle").style("font-size", "1.1em").attr("text-anchor", "middle").attr("transform", subTransformStr).attr("fill", this.textColor).text(plotDim.subtitle.text.length > 80 ? plotDim.subtitle.text.slice(0, 80) + "..." : plotDim.subtitle.text);
735
- }
736
- }
737
- renderAxis(plotDim, dom, scale, settings) {
738
- if (settings.isVertical) scale.range([scale.range()[1], scale.range()[0]]);
739
- const ticks = scale.ticks();
740
- const tickValues = plotDim.axis.values(ticks);
741
- dom.axis.attr("class", "sjpp-boxplot-axis").attr("transform", `translate(${plotDim.axis.x}, ${plotDim.axis.y})`).transition().call(
742
- settings.isVertical ? axisLeft(scale).tickValues(tickValues).tickFormat((d) => plotDim.axis.format(d)).tickPadding(8) : axisTop(scale).tickValues(tickValues).tickFormat((d) => plotDim.axis.format(d))
743
- );
744
- axisstyle({
745
- axis: dom.axis,
746
- showline: true,
747
- fontsize: 12,
748
- color: this.textColor
749
- });
750
- }
751
- renderBoxPlots(dom, chart, scale, settings) {
752
- for (const plot of chart.plots) {
753
- const g = dom.boxplots.append("g").attr("class", "sjpp-boxplot-plot").attr("padding", "5px");
754
- drawBoxplot({
755
- bp: plot.boxplot,
756
- g,
757
- color: settings.displayMode == "filled" ? "black" : plot.color,
758
- scale,
759
- rowheight: settings.rowHeight,
760
- labpad: settings.labelPad,
761
- labColor: this.textColor
762
- });
763
- const transformStr = `translate(${plot.x}, ${plot.y})${settings.isVertical ? `, rotate(-90)` : ""}`;
764
- g.attr("transform", transformStr);
765
- if (settings.isVertical) {
766
- g.select("text").attr("transform", "rotate(45)");
767
- }
768
- new BoxPlotToolTips(plot, g, dom.tip, settings.isVertical);
769
- const numCollection = isNumTermCollection(this.interactions.getPlotConfig().term.term);
770
- if (!numCollection && chart.plots.length > 1) {
771
- const labelMenuTip = new Menu({ padding: "" });
772
- new BoxPlotLabelMenu(
773
- plot,
774
- this.app,
775
- this.interactions,
776
- labelMenuTip,
777
- settings.isVertical
778
- /*chart*/
779
- );
780
- }
781
- }
782
- }
783
- };
784
-
785
- // plots/boxplot/view/View.ts
786
- var View = class {
787
- constructor(viewData, settings, dom, app, interactions) {
788
- this.app = app;
789
- this.dom = dom;
790
- this.interactions = interactions;
791
- this.settings = settings;
792
- if (!viewData || !viewData.charts) return;
793
- dom.div.style("background-color", viewData.backgroundColor);
794
- for (const chart of Object.values(viewData.charts)) {
795
- const chartWrapper = dom.charts.append("div").attr("class", "sjpp-boxplot-chart-wrapper");
796
- const svg = chartWrapper.append("svg").attr("class", "sjpp-boxplot-svg");
797
- chart["svg"] = svg;
798
- const chartDom = {
799
- svg,
800
- tip: dom.tip
801
- };
802
- if (chart.plotDim.subtitle.text) {
803
- chartDom.subtitle = svg.append("text");
804
- }
805
- chartDom.title = svg.append("text");
806
- chartDom.axis = svg.append("g");
807
- chartDom.boxplots = svg.append("g").attr("class", "sjpp-boxplot-boxplots");
808
- if (chart.wilcoxon) {
809
- chartDom.assocTableDiv = chartWrapper.append("div").attr("class", "sjpp-boxplot-wilcoxon").style("display", "inline-block");
810
- }
811
- new ChartRender(
812
- chartDom,
813
- this.settings,
814
- this.app,
815
- this.interactions,
816
- chart,
817
- viewData.backgroundColor,
818
- viewData.textColor
819
- );
820
- }
821
- new LegendRenderer(dom.legend, viewData.legend, interactions, viewData.textColor);
822
- }
823
- };
824
-
825
- // plots/boxplot/BoxPlotControlInputs.ts
826
- function setBoxPlotControlInputs(state, app, opts, getCharts, useDefaultSettings) {
827
- const controlLabels = state.config.controlLabels;
828
- if (!controlLabels) throw new Error("controls labels not found");
829
- const specialCase = getSingleCellSpecialCase(state.config);
830
- const inputs = [
831
- {
832
- type: "term",
833
- configKey: "term",
834
- chartType: "boxplot",
835
- usecase: { target: "boxplot", detail: "term" },
836
- label: controlLabels.term1?.label || renderTerm1Label,
837
- vocabApi: app.vocabApi,
838
- menuOptions: "edit",
839
- // Hide term1 control for termCollection; later reenable when tw edit menu works to allow choosing subset of member terms
840
- // and take into account state changes.
841
- getDisplayStyle: (plot) => isNumTermCollection(plot.config.term?.term) ? "none" : ""
842
- },
843
- {
844
- type: "term",
845
- configKey: "term2",
846
- chartType: "boxplot",
847
- usecase: { target: "boxplot", detail: "term2", specialCase },
848
- title: controlLabels.term2.title || controlLabels.term2.label,
849
- label: controlLabels.term2.label,
850
- vocabApi: app.vocabApi,
851
- numericEditMenuVersion: opts.numericEditMenuVersion || ["continuous", "discrete"],
852
- defaultQ4fillTW: getT0T2defaultQ(),
853
- // Hide term2 control when numeric termCollection is detected
854
- // and take into account state changes.
855
- getDisplayStyle: (plot) => isNumTermCollection(plot.config.term?.term) ? "none" : ""
856
- },
857
- {
858
- type: "term",
859
- configKey: "term0",
860
- chartType: "boxplot",
861
- usecase: { target: "boxplot", detail: "term0", specialCase },
862
- title: controlLabels.term0.title || controlLabels.term0.label,
863
- label: controlLabels.term0.label,
864
- vocabApi: app.vocabApi,
865
- // by default, do not allow continuous mode for divide-by term, since
866
- // it will create a separate violin-overlay group per unique float or integer value
867
- // and there will nonsensical tens/hundreds of these charts based on the cohort size
868
- numericEditMenuVersion: opts.numericEditMenuVersion || ["discrete"],
869
- defaultQ4fillTW: getT0T2defaultQ(),
870
- // Hide term0 control when numeric termCollection is detected
871
- // and take into account state changes.
872
- getDisplayStyle: (plot) => isNumTermCollection(plot.config.term?.term) ? "none" : ""
873
- },
874
- {
875
- label: "Order by",
876
- title: "Order box plots by parameters",
877
- type: "radio",
878
- chartType: "boxplot",
879
- settingsKey: "orderByMedian",
880
- options: [
881
- { label: "Default", value: false },
882
- { label: "Median values", value: true }
883
- ],
884
- getDisplayStyle: () => {
885
- const charts = getCharts();
886
- let style = "none";
887
- for (const k of Object.keys(charts)) {
888
- const chart = charts[k];
889
- if (chart.plots.length > 1) style = "";
890
- }
891
- return style;
892
- }
893
- },
894
- {
895
- label: "Scale",
896
- title: "Change the axis scale",
897
- type: "radio",
898
- chartType: "boxplot",
899
- settingsKey: "isLogScale",
900
- options: [
901
- { label: "Linear", value: false },
902
- { label: "Log10", value: true }
903
- ]
904
- },
905
- {
906
- label: "Orientation",
907
- title: "Change the orientation of the box plots",
908
- type: "radio",
909
- chartType: "boxplot",
910
- settingsKey: "isVertical",
911
- options: [
912
- { label: "Horizontal", value: false },
913
- { label: "Vertical", value: true }
914
- ]
915
- },
916
- {
917
- label: "Plot length",
918
- title: "Set the plot length of the entire plot in pixels, >=200",
919
- type: "number",
920
- chartType: "boxplot",
921
- settingsKey: "plotLength",
922
- debounceInterval: 500,
923
- min: 200,
924
- step: 10
925
- },
926
- {
927
- label: "Box size",
928
- title: "Set the box size or thickness in pixels of each box plot between 20 and 50",
929
- type: "number",
930
- chartType: "boxplot",
931
- settingsKey: "rowHeight",
932
- step: 1,
933
- max: 50,
934
- min: 20,
935
- debounceInterval: 500,
936
- processInput: (val) => {
937
- if (useDefaultSettings == true) useDefaultSettings = false;
938
- return val;
939
- }
940
- },
941
- {
942
- label: "Plots padding",
943
- title: "Set the space between each box plot. Number must be between 10 and 20",
944
- type: "number",
945
- chartType: "boxplot",
946
- settingsKey: "rowSpace",
947
- step: 1,
948
- max: 20,
949
- min: 10,
950
- debounceInterval: 500,
951
- processInput: (val) => {
952
- if (useDefaultSettings == true) useDefaultSettings = false;
953
- return val;
954
- }
955
- },
956
- {
957
- label: "Default color",
958
- type: "color",
959
- chartType: "boxplot",
960
- settingsKey: "color",
961
- getDisplayStyle: () => {
962
- const charts = getCharts();
963
- let style = "";
964
- for (const k of Object.keys(charts)) {
965
- const chart = charts[k];
966
- if (chart.plots.length > 1) style = "none";
967
- }
968
- return style;
969
- }
970
- },
971
- {
972
- label: "Display mode",
973
- title: "Apply a dark theme to the plot",
974
- type: "radio",
975
- chartType: "boxplot",
976
- settingsKey: "displayMode",
977
- options: [
978
- { label: "Default", value: "default" },
979
- { label: "Filled", value: "filled" },
980
- { label: "Dark mode", value: "dark" }
981
- ]
982
- },
983
- {
984
- label: "Show association tests",
985
- boxLabel: "",
986
- type: "checkbox",
987
- chartType: "boxplot",
988
- settingsKey: "showAssocTests",
989
- title: `Show association tests next to the box plots.`,
990
- getDisplayStyle: (plot) => {
991
- return plot?.term2 ? "" : "none";
992
- }
993
- },
994
- {
995
- label: "Pairwise test groups",
996
- title: `The most groups, the largest ones, that get the pairwise Wilcoxon tests, from 2 to ${pairwiseTestGroupsLimit}`,
997
- type: "number",
998
- chartType: "boxplot",
999
- settingsKey: "maxPairwiseTestGroups",
1000
- step: 1,
1001
- min: 2,
1002
- max: pairwiseTestGroupsLimit,
1003
- debounceInterval: 500,
1004
- processInput: (val) => Math.round(val),
1005
- getDisplayStyle: (plot) => plot?.term2 || plot?.term?.term?.type === "termCollection" && plot.term.term.memberType === "numeric" && plot.term.type !== "TermCollectionTWFraction" ? "" : "none"
1006
- }
1007
- ];
1008
- if (state.termdbConfig?.boxplots?.removeOutliers) {
1009
- inputs.push({
1010
- label: "Remove outliers",
1011
- boxLabel: "",
1012
- type: "checkbox",
1013
- chartType: "boxplot",
1014
- settingsKey: "removeOutliers",
1015
- title: `Option to remove outliers from the analysis`
1016
- });
1017
- }
1018
- return inputs;
1019
- }
1020
-
1021
- // plots/boxplot/BoxPlot.ts
1022
- var TdbBoxplot = class _TdbBoxplot extends PlotBase {
1023
- constructor(opts, api) {
1024
- super(opts, api);
1025
- this.useDefaultSettings = true;
1026
- this.configTermKeys = ["term", "term0", "term2"];
1027
- this.type = _TdbBoxplot.type;
1028
- this.components = {
1029
- controls: {}
1030
- };
1031
- const holder = opts.holder.classed("sjpp-boxplot-main", true);
1032
- const { controls, errdiv, loadingDiv, mainDiv, renderedData, charts, legendDiv } = this.getStandardDomLayout(
1033
- holder,
1034
- opts
1035
- );
1036
- this.dom = {
1037
- controls,
1038
- div: mainDiv,
1039
- error: errdiv,
1040
- loading: loadingDiv,
1041
- renderedData,
1042
- charts: charts.attr("class", "sjpp-boxplot-charts").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("max-width", "100vw"),
1043
- legend: legendDiv.append("div").attr("class", "sjpp-boxplot-legend").style("margin-top", "25px"),
1044
- tip: new Menu()
1045
- };
1046
- if (opts.header) this.dom.header = opts.header.html("Box plot");
1047
- }
1048
- static {
1049
- this.type = "boxplot";
1050
- }
1051
- async setControls() {
1052
- const state = this.getState(this.app.getState());
1053
- const inputs = setBoxPlotControlInputs(
1054
- state,
1055
- this.app,
1056
- this.opts,
1057
- () => {
1058
- return this.data?.charts || [];
1059
- },
1060
- this.useDefaultSettings
1061
- );
1062
- this.components.controls = await controlsInit({
1063
- app: this.app,
1064
- id: this.id,
1065
- holder: this.dom.controls.style("display", "inline-block"),
1066
- inputs
1067
- });
1068
- this.components.controls.on("downloadClick.boxplot", (event) => {
1069
- this.download(event);
1070
- });
1071
- this.components.controls.on("helpClick.boxplot", () => {
1072
- this.interactions.help();
1073
- });
1074
- if (state.termdbConfig?.hidePlotDocumentation) {
1075
- this.dom.controls.select('div[aria-label="Documentation"]').remove();
1076
- }
1077
- }
1078
- reactsTo(action) {
1079
- if (action.type.startsWith("plot_")) {
1080
- return (action.id === this.id || action.id == this.parentId) && (!action.config?.childType || action.config?.childType == this.type);
1081
- }
1082
- return true;
1083
- }
1084
- getState(appState) {
1085
- const config = appState.plots.find((p) => p.id === this.id);
1086
- if (!config) {
1087
- throw new Error(
1088
- `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`
1089
- );
1090
- }
1091
- const parentConfig = appState.plots.find((p) => p.id === this.parentId);
1092
- const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
1093
- return {
1094
- termdbConfig: appState.termdbConfig,
1095
- termfilter,
1096
- vocab: appState.vocab,
1097
- config: Object.assign({}, config, {
1098
- settings: {
1099
- boxplot: config.settings.boxplot
1100
- }
1101
- })
1102
- };
1103
- }
1104
- async init() {
1105
- this.dom.div.style("display", "inline-block").style("margin-left", "20px");
1106
- this.interactions = new BoxPlotInteractions(this, () => this.data);
1107
- await this.setControls();
1108
- }
1109
- async main() {
1110
- const c = this.state.config;
1111
- if (c.childType != this.type && c.chartType != this.type) return;
1112
- if (!this.interactions) throw new Error("Interactions not initialized [box plot main()]");
1113
- const config = await this.getMutableConfig();
1114
- const settings = config.settings.boxplot;
1115
- const model = new Model(this, config);
1116
- try {
1117
- this.toggleLoadingDiv("block", "block");
1118
- const data = await model.getData();
1119
- if (isErrorResponse(data)) throw new Error(data.error);
1120
- setDescrStatsByTerm([config.term, config.term2], data.descrStats);
1121
- config.bins = data.bins;
1122
- if (!data.charts || !Object.keys(data.charts).length) {
1123
- this.interactions.clearDom();
1124
- this.dom.error.style("padding", "20px 20px 20px 60px").text("No visible box plot data to render");
1125
- this.toggleLoadingDiv("none");
1126
- return;
1127
- }
1128
- this.data = data;
1129
- } catch (e) {
1130
- this.toggleLoadingDiv("none", "none");
1131
- if (this.app.isAbortError(e)) return;
1132
- if (e.stack) console.log(e.stack);
1133
- if (e instanceof Error) console.error(e.message || e);
1134
- throw new Error(e);
1135
- }
1136
- this.interactions.clearDom();
1137
- const labels = Object.values(this.data.charts).reduce((labels2, chart) => {
1138
- const chartLabels = chart.plots.filter((p) => !p.isHidden).map((p) => p.boxplot.label);
1139
- labels2.push(...chartLabels);
1140
- return labels2;
1141
- }, []);
1142
- const tempsvg = this.dom.charts.append("svg");
1143
- const maxLabelLgth = getMaxLabelWidth(tempsvg.append("g"), labels);
1144
- tempsvg.remove();
1145
- const viewModel = new ViewModel(config, this.data, settings, maxLabelLgth, this.useDefaultSettings);
1146
- if (!viewModel.viewData) throw new Error("No viewData from ViewModel");
1147
- if ((viewModel.rowSpace !== settings.rowSpace || viewModel.rowHeight !== settings.rowHeight) && this.useDefaultSettings == true) {
1148
- settings.rowSpace = viewModel.rowSpace;
1149
- settings.rowHeight = viewModel.rowHeight;
1150
- this.app.save({
1151
- type: "plot_edit",
1152
- id: this.id,
1153
- config: {
1154
- settings: {
1155
- boxplot: {
1156
- rowSpace: viewModel.rowSpace,
1157
- rowHeight: viewModel.rowHeight
1158
- }
1159
- }
1160
- }
1161
- });
1162
- }
1163
- this.toggleLoadingDiv("none");
1164
- this.dom.renderedData.style("display", "");
1165
- new View(viewModel.viewData, settings, this.dom, this.app, this.interactions);
1166
- this.data.charts = viewModel.viewData.charts;
1167
- }
1168
- getChartImages() {
1169
- const chartImages = [];
1170
- const charts = this.data.charts;
1171
- for (const [key, chart] of Object.entries(charts)) {
1172
- const svg = chart.svg;
1173
- const title = getChartTitle(this.state.config, key);
1174
- const name = `${this.state.config.term.term.name} ${title}`;
1175
- chartImages.push({ name, svg });
1176
- }
1177
- return chartImages;
1178
- }
1179
- download(event) {
1180
- if (!this.state) return;
1181
- const config = this.state.config;
1182
- const name2svg = this.getChartImages();
1183
- const filename = config.term.term.name;
1184
- const extraOptions = [];
1185
- const descrStatsByTerm = this.data?.descrStats || {};
1186
- const statTerms = [config.term, config.term2].filter(
1187
- (tw) => tw?.$id && descrStatsByTerm[tw.$id] && tw.term.type != "termCollection"
1188
- );
1189
- if (statTerms.length) {
1190
- extraOptions.push({
1191
- label: "Descriptive statistics",
1192
- testid: "sjpp-download-descrstats",
1193
- filename: `${filename}_descriptive_stats`,
1194
- callback: () => descrStatsToTSV(statTerms.map((tw) => ({ name: tw.term.name, stats: descrStatsByTerm[tw.$id] })))
1195
- });
1196
- }
1197
- const charts = Object.entries(this.data?.charts || {});
1198
- if (charts.some(([, chart]) => chart.wilcoxon?.length)) {
1199
- extraOptions.push({
1200
- label: "Group comparisons",
1201
- testid: "sjpp-download-comparison",
1202
- filename: `${filename}_wilcoxon_group_comparisons`,
1203
- callback: () => testRowsToTSV(
1204
- "Wilcoxon's rank sum test",
1205
- ["Group 1", "Group 2", "P-value"],
1206
- charts.filter(([, chart]) => chart.wilcoxon).map(([chartId, chart]) => ({ chartLabel: getChartTitle(config, chartId), rows: chart.wilcoxon }))
1207
- )
1208
- });
1209
- }
1210
- const dm = new CustomDownloadMenu({ chartImages: name2svg, filename, extraOptions });
1211
- dm.show(event.clientX, event.clientY, event.target);
1212
- }
1213
- };
1214
- var boxplotInit = getCompInit(TdbBoxplot);
1215
- var componentInit = boxplotInit;
1216
- async function getPlotConfig(opts, app) {
1217
- try {
1218
- if (!opts.term) throw new Error("opts.term{} missing");
1219
- if (opts.term.term?.type == "termCollection") {
1220
- }
1221
- await fillTermWrapper(opts.term, app.vocabApi);
1222
- if (opts.term2) await fillTermWrapper(opts.term2, app.vocabApi);
1223
- if (opts.term0) await fillTermWrapper(opts.term0, app.vocabApi);
1224
- } catch (e) {
1225
- console.error(new Error(`${e} [boxplot getPlotConfig()]`));
1226
- throw new Error(`boxplot getPlotConfig() failed`);
1227
- }
1228
- const config = {
1229
- id: opts.term.term.id || opts.term.$id,
1230
- controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {}),
1231
- settings: {
1232
- controls: {
1233
- term2: null,
1234
- term0: null
1235
- },
1236
- boxplot: getDefaultBoxplotSettings(app, opts.overrides || {})
1237
- }
1238
- };
1239
- return copyMerge(config, opts);
1240
- }
1241
- export {
1242
- TdbBoxplot,
1243
- boxplotInit,
1244
- componentInit,
1245
- getPlotConfig
1246
- };
1247
- //# sourceMappingURL=BoxPlot-JTBQA6PL.js.map