@sjcrh/proteinpaint-client 2.203.0 → 2.203.1

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 (884) hide show
  1. package/dist/2dmaf-6CEBP4SA.js +1366 -0
  2. package/dist/AIProjectAdmin-2CKKFC3A.js +951 -0
  3. package/dist/AggregateMatrix-5TBUMFE5.js +665 -0
  4. package/dist/AppHeader-5YBPWF44.js +829 -0
  5. package/dist/BoxPlot-UOJS5SJV.js +1210 -0
  6. package/dist/CorrelationVolcano-KX6JPZMT.js +613 -0
  7. package/dist/Cuminc-TLOOLZWR.js +1208 -0
  8. package/dist/DE-HUQLQ2Z3.js +87 -0
  9. package/dist/DEinput-WWUISAF2.js +404 -0
  10. package/dist/DifferentialAnalysis-6DTAGCEY.js +237 -0
  11. package/dist/Disco-P6ZLPYLF.js +3388 -0
  12. package/dist/Disco.UI-WGTMAFK2.js +242 -0
  13. package/dist/DmrPlot-3FRU5KUK.js +636 -0
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  15. package/dist/GSEA-DEEUAAMI.js +850 -0
  16. package/dist/GeneExpInput-6QWGEAFV.js +361 -0
  17. package/dist/Geomap-6HT2B7RH.js +83 -0
  18. package/dist/HicApp-PCNOUULF.js +2244 -0
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  36. package/dist/ProteomeInput-PRS3DEMZ.js +387 -0
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  153. package/dist/cohort-U7M6Q2UX.js +69 -0
  154. package/dist/condition-EGAV2PMJ.js +326 -0
  155. package/dist/controls-PTMYWUZV.js +33 -0
  156. package/dist/controls.config-DOA6PTP2.js +33 -0
  157. package/dist/correlation-Y3EL6GB7.js +94 -0
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  159. package/dist/dataDownload-EQGUAOK2.js +328 -0
  160. package/dist/databrowser.ui-ABGOJUWQ.js +424 -0
  161. package/dist/dictionary-YOLLEDE5.js +112 -0
  162. package/dist/dnaMethylation-JZT63UHO.js +32 -0
  163. package/dist/dnaMethylation.integration.spec-EATCABJW.js +197 -0
  164. package/dist/dofetch-YNBIUFV5.js +48 -0
  165. package/dist/e2pca-RD6COCRL.js +343 -0
  166. package/dist/ep-BAI7WUET.js +1248 -0
  167. package/dist/expclust.gdc.spec-LKV2CQA5.js +301 -0
  168. package/dist/facet-X3SXQIAC.js +518 -0
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  170. package/dist/geneExpClustering-BJD5U3KG.js +243 -0
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  180. package/dist/genefusion.ui-4T5R7DT7.js +302 -0
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  183. package/dist/grin2-EXBG7TMS.js +1136 -0
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  240. package/dist/proteinView-7GWHQYXC.js +1561 -0
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  818. /package/dist/{polar2-JKV74QV5.js.map → polar2-AB6SVYRS.js.map} +0 -0
  819. /package/dist/{profileForms-VDYCFH4M.js.map → profileForms-AIEHZ4GC.js.map} +0 -0
  820. /package/dist/{plot.app-MOIVGIS6.js.map → profilePlot-PZDFGXKZ.js.map} +0 -0
  821. /package/dist/{proteinView-A3EM6OR5.js.map → proteinView-7GWHQYXC.js.map} +0 -0
  822. /package/dist/{pseudbulk.unit.spec-CUMTLAH7.js.map → pseudbulk.unit.spec-NFT4VNTI.js.map} +0 -0
  823. /package/dist/{profilePlot-PR3LVRYU.js.map → pseudobulk-WDGWTXW4.js.map} +0 -0
  824. /package/dist/{pseudobulk-5E5MSMU3.js.map → qualitative-PZYJENE7.js.map} +0 -0
  825. /package/dist/{radar2-A5OYMORS.js.map → radar2-QHRGH3YS.js.map} +0 -0
  826. /package/dist/{radarFacility2-4TPJB6M4.js.map → radarFacility2-2JD26FL6.js.map} +0 -0
  827. /package/dist/{qualitative-WPXUBISK.js.map → render-YA4Z56LT.js.map} +0 -0
  828. /package/dist/{report-NCJOTYIC.js.map → report-2NUKFJTF.js.map} +0 -0
  829. /package/dist/{render-XQBWWS33.js.map → sampleView-2XVPJTVR.js.map} +0 -0
  830. /package/dist/{samplelst-FV7BAUN5.js.map → samplelst-DMILFDT5.js.map} +0 -0
  831. /package/dist/{samplematrix-DFD3PNI4.js.map → samplematrix-LYA5XTUM.js.map} +0 -0
  832. /package/dist/{sc-GIMTDVLG.js.map → sc-CM2C34MN.js.map} +0 -0
  833. /package/dist/{scatter-4GJ5HKUY.js.map → scatter-C3CH3HTF.js.map} +0 -0
  834. /package/dist/{scatter-P3ISZB3R.js.map → scatter-GO6LV6NY.js.map} +0 -0
  835. /package/dist/{selectGenomeWithTklst-ZZ4CEHDU.js.map → selectGenomeWithTklst-5C7UBTGZ.js.map} +0 -0
  836. /package/dist/{sampleView-2PUSMG4W.js.map → singleCellCellType-EZYESBVZ.js.map} +0 -0
  837. /package/dist/{singleCellCellType.unit.spec-JNEIICK5.js.map → singleCellCellType.unit.spec-DB6FM4XR.js.map} +0 -0
  838. /package/dist/{singleCellCellType-CEERCVTR.js.map → singleCellGeneExpression-DZLEFPW4.js.map} +0 -0
  839. /package/dist/{singleCellGeneExpression.unit.spec-CGRZGY66.js.map → singleCellGeneExpression.unit.spec-ZTBK3V43.js.map} +0 -0
  840. /package/dist/{singleCellGeneExpression-G5B7DDES.js.map → singleCellPlot-VF4TZ4FT.js.map} +0 -0
  841. /package/dist/{singlecell-IPTSIKNA.js.map → singlecell-2MHROPBN.js.map} +0 -0
  842. /package/dist/{singlecell-VB4KLPJF.js.map → singlecell-GPAFNOUZ.js.map} +0 -0
  843. /package/dist/{singleCellPlot-US5KTHS4.js.map → snp-K4EAEVW4.js.map} +0 -0
  844. /package/dist/{snp.unit.spec-Q537NGVG.js.map → snp.unit.spec-BUVQLVOY.js.map} +0 -0
  845. /package/dist/{snplocus-BV6WJTVP.js.map → snplocus-GEVISN6Z.js.map} +0 -0
  846. /package/dist/{spliceevent.a53ss.diagram-3BUQVK4Q.js.map → spliceevent.a53ss.diagram-5UPWNAZF.js.map} +0 -0
  847. /package/dist/{spliceevent.exonskip.diagram-CQZ2DFQ5.js.map → spliceevent.exonskip.diagram-7TKAQURC.js.map} +0 -0
  848. /package/dist/{spliceevent.noeventdiagram-QAEPR6LD.js.map → spliceevent.noeventdiagram-CDXZLR3Z.js.map} +0 -0
  849. /package/dist/{snp-6V2SCCRN.js.map → ssGSEA-NMCJUQXT.js.map} +0 -0
  850. /package/dist/{ssGSEA.unit.spec-A337IMC7.js.map → ssGSEA.unit.spec-3FQALTPQ.js.map} +0 -0
  851. /package/dist/{stattable-J4ZQKJFM.js.map → stattable-2RXQPWKK.js.map} +0 -0
  852. /package/dist/{summarizeCnvGeneexp-76UJXLA4.js.map → summarizeCnvGeneexp-4BQS5AFM.js.map} +0 -0
  853. /package/dist/{summarizeGeneexpSurvival-ZUEHXA2R.js.map → summarizeGeneexpSurvival-HTBZQFB5.js.map} +0 -0
  854. /package/dist/{summarizeMutationCnv-EBCBVMG6.js.map → summarizeMutationCnv-XUWZGPCM.js.map} +0 -0
  855. /package/dist/{ssGSEA-XNI5S7AC.js.map → summarizeMutationDiagnosis-QUJX42TO.js.map} +0 -0
  856. /package/dist/{summarizeMutationSurvival-QRFMJLLO.js.map → summarizeMutationSurvival-3R47TTR6.js.map} +0 -0
  857. /package/dist/{summarizeMutationDiagnosis-VLFI2ZIZ.js.map → summary-6UUB63QR.js.map} +0 -0
  858. /package/dist/{summary.integration.spec-52WP6SNY.js.map → summary.integration.spec-JJDE6SRV.js.map} +0 -0
  859. /package/dist/{summaryInput-WUJNHCGH.js.map → summaryInput-JG4AW6FW.js.map} +0 -0
  860. /package/dist/{sunburst-IJ3ZG2BC.js.map → sunburst-YKB42RZX.js.map} +0 -0
  861. /package/dist/{survival-SQRYWGWZ.js.map → survival-3IFFTDQA.js.map} +0 -0
  862. /package/dist/{survival-F2B5JKOO.js.map → survival-HOFNJENX.js.map} +0 -0
  863. /package/dist/{svgraph-HVCMF6KI.js.map → svgraph-WFEY4ZIZ.js.map} +0 -0
  864. /package/dist/{svmr-PROHTMTP.js.map → svmr-44EIX7YD.js.map} +0 -0
  865. /package/dist/{table-3E64OJNV.js.map → table-6MKVJUNC.js.map} +0 -0
  866. /package/dist/{termCollection-WKT6ESMI.js.map → termCollection-6JBVQL6Y.js.map} +0 -0
  867. /package/dist/{summary-U3YKEMZC.js.map → termCollection-TTELZVC5.js.map} +0 -0
  868. /package/dist/{termCollection.unit.spec-XMOCMVER.js.map → termCollection.unit.spec-6Z7X646L.js.map} +0 -0
  869. /package/dist/{termCollection-MUH7P6B5.js.map → termCollectionFractionSelection-5DVIJBM5.js.map} +0 -0
  870. /package/dist/{termCollectionFractionSelection.unit.spec-MG7E3EIZ.js.map → termCollectionFractionSelection.unit.spec-3HIM5BIF.js.map} +0 -0
  871. /package/dist/{termCollectionFractionSelection-P5G6WIJJ.js.map → tk-HSYWJCGQ.js.map} +0 -0
  872. /package/dist/{tk-HWUPUGOS.js.map → tk-PNOVG2XS.js.map} +0 -0
  873. /package/dist/{tp.ui-RRB5MJRD.js.map → tp.ui-COBBSUPB.js.map} +0 -0
  874. /package/dist/{tk-SBM2GN3S.js.map → tvs.dt-35AKURFI.js.map} +0 -0
  875. /package/dist/{tvs.dtcnv.categorical-7RJPQKMX.js.map → tvs.dtcnv.categorical-3EHXYROL.js.map} +0 -0
  876. /package/dist/{tvs.dtcnv.continuous-FW4ZXIYY.js.map → tvs.dtcnv.continuous-AXQ2GU6S.js.map} +0 -0
  877. /package/dist/{tvs.dtfusion-3GDWW3ML.js.map → tvs.dtfusion-PLJIMPNX.js.map} +0 -0
  878. /package/dist/{tvs.dtitd-FER4H4UO.js.map → tvs.dtitd-JS6RFBV5.js.map} +0 -0
  879. /package/dist/{tvs.dtsnvindel-ISEOJ5UA.js.map → tvs.dtsnvindel-MDEM5MPT.js.map} +0 -0
  880. /package/dist/{tvs.dtsv-JDML7EWE.js.map → tvs.dtsv-OU756YLO.js.map} +0 -0
  881. /package/dist/{tvs.samplelst-MJTM6GSV.js.map → tvs.samplelst-5NDICES4.js.map} +0 -0
  882. /package/dist/{tvs.termCollection-GMOXBJWF.js.map → tvs.termCollection-5URPDPH6.js.map} +0 -0
  883. /package/dist/{tvs.dt-I2ECKHQ2.js.map → vocabulary-CHCVMPK5.js.map} +0 -0
  884. /package/dist/{wsi.direct-IVPACPNT.js.map → wsi.direct-JSKV4H4X.js.map} +0 -0
@@ -0,0 +1,665 @@
1
+ import {
2
+ ColorScale,
3
+ DownloadMenu,
4
+ LegendCircleReference,
5
+ PlotBase,
6
+ capitalizeFirstLetter,
7
+ controlsInit,
8
+ getCombinedTermFilter,
9
+ getMaxLabelWidth,
10
+ table2col
11
+ } from "./chunk-D5PX2UDG.js";
12
+ import "./chunk-HJ6L54YS.js";
13
+ import "./chunk-XFAL46LZ.js";
14
+ import "./chunk-OPMMU6DQ.js";
15
+ import {
16
+ Menu
17
+ } from "./chunk-ELJX3QIQ.js";
18
+ import "./chunk-7BLXK3GI.js";
19
+ import "./chunk-VSSZJHOR.js";
20
+ import "./chunk-5RUVBYLK.js";
21
+ import "./chunk-6X7PP7A4.js";
22
+ import "./chunk-EO6M3LY3.js";
23
+ import "./chunk-DXLO4OAB.js";
24
+ import {
25
+ PSEUDOBULK
26
+ } from "./chunk-4QBRVM4V.js";
27
+ import {
28
+ copyMerge,
29
+ getCompInit
30
+ } from "./chunk-H6INPPUC.js";
31
+ import "./chunk-PF4DSFDR.js";
32
+ import "./chunk-IMYSFDE5.js";
33
+ import "./chunk-W5J3LTYS.js";
34
+ import "./chunk-4ZL6IBXM.js";
35
+ import {
36
+ linear
37
+ } from "./chunk-OZVWP4ZR.js";
38
+ import "./chunk-FXQXCOII.js";
39
+ import {
40
+ roundValueAuto
41
+ } from "./chunk-TLT4YIG3.js";
42
+ import "./chunk-5R63Q5KH.js";
43
+ import "./chunk-I6Y4O3RR.js";
44
+ import {
45
+ rgb
46
+ } from "./chunk-Q5RDQNIT.js";
47
+ import "./chunk-DQC5FFGV.js";
48
+ import "./chunk-HFNDKYVF.js";
49
+
50
+ // plots/aggregateMatrix/model/AggMatrixModel.ts
51
+ var AggMatrixModel = class {
52
+ constructor(ag) {
53
+ this.ag = ag;
54
+ this.app = ag.app;
55
+ }
56
+ async getData() {
57
+ const state = this.ag.state;
58
+ const config = structuredClone(state.config);
59
+ validatePlotConfig(config);
60
+ const settings = config.settings.aggregateMatrix || {};
61
+ const body = {
62
+ rows: config.rows,
63
+ columns: config.columns,
64
+ gradientMethod: settings.gradientMethod,
65
+ sizeMethod: settings.sizeMethod,
66
+ minDotSize: settings.minDotSize,
67
+ maxDotSize: settings.maxDotSize,
68
+ filter: state.termfilter.filter,
69
+ filter0: state.termfilter.filter0,
70
+ signal: this.ag.api?.getAbortSignal()
71
+ };
72
+ return await this.app.vocabApi.getAggregateMatrixData(body);
73
+ }
74
+ };
75
+
76
+ // plots/aggregateMatrix/settings/defaults.ts
77
+ function getAggregateMatrixSettings(overrides = {}) {
78
+ const defaults = {
79
+ startColor: "#ff9400",
80
+ stopColor: "#0080ff",
81
+ gradientMethod: "mean",
82
+ sizeMethod: "mean",
83
+ minDotSize: 5,
84
+ maxDotSize: 20,
85
+ dotInputMin: 2,
86
+ dotInputMax: 35
87
+ };
88
+ const mergedSettings = Object.assign({}, defaults, overrides);
89
+ const isValidMinMax = validateMinMax(mergedSettings, mergedSettings.minDotSize, mergedSettings.maxDotSize);
90
+ if (isValidMinMax !== null) {
91
+ throw new Error(`Invalid min/max dot size settings: ${isValidMinMax}`);
92
+ }
93
+ return mergedSettings;
94
+ }
95
+ function validateMinMax(settings, min, max) {
96
+ if (min < settings.dotInputMin) {
97
+ return `Minimum dot size must be greater than or equal to ${settings.dotInputMin}`;
98
+ }
99
+ if (max > settings.dotInputMax) {
100
+ return `Maximum dot size must be less than or equal to ${settings.dotInputMax}`;
101
+ }
102
+ if (min > max) {
103
+ return `Minimum dot size must be less than or equal to maximum dot size`;
104
+ }
105
+ if (max < min) {
106
+ return `Maximum dot size must be greater than or equal to minimum dot size`;
107
+ }
108
+ return null;
109
+ }
110
+
111
+ // plots/aggregateMatrix/viewModel/AggMatrixViewModel.ts
112
+ var AggMatrixViewModel = class {
113
+ constructor(ag) {
114
+ this.rowSectionRotateFlags = [];
115
+ this.colSectionRotateFlags = [];
116
+ this.topPad = 20;
117
+ this.hoziPad = 20;
118
+ this.bottomPad = 20;
119
+ this.sectionGap = 8;
120
+ this.colSectionGap = 4;
121
+ this.minColSectionLineInset = 2;
122
+ this.colSectionLabelLineGap = 3;
123
+ this.colSectionLabelGap = 8;
124
+ this.labelFontPx = 12;
125
+ this.ag = ag;
126
+ }
127
+ processData(data) {
128
+ this.viewData = this.getDefaultViewData();
129
+ const settings = this.ag.state.config.settings.aggregateMatrix;
130
+ const dotPadding = settings.maxDotSize * 1.5;
131
+ const cellSize = settings.maxDotSize + dotPadding;
132
+ const measureSvg = this.ag.dom.mainDiv.append("svg");
133
+ const rowData = data.axesLayout.rows;
134
+ this.rowTermLabelLgth = getMaxLabelWidth(measureSvg, [rowData.longestLabel]);
135
+ const rowSectionLayout = this.getSectionLabelLayout(rowData.sections, cellSize, measureSvg, true);
136
+ this.rowSectionRotateFlags = rowSectionLayout.rotateFlags;
137
+ this.maxRowSectionLabelWdth = rowSectionLayout.maxCrossAxisSpace;
138
+ this.maxRowLabelLgth = this.rowTermLabelLgth + (this.maxRowSectionLabelWdth ? this.sectionGap + this.maxRowSectionLabelWdth : 0);
139
+ this.totalRowHght = cellSize * rowData.rowCount;
140
+ const colData = data.axesLayout.columns;
141
+ this.colTermLabelLgth = getMaxLabelWidth(measureSvg, [colData.longestLabel]);
142
+ const colSectionLayout = this.getSectionLabelLayout(colData.sections, cellSize, measureSvg, false);
143
+ this.colSectionRotateFlags = colSectionLayout.rotateFlags;
144
+ this.maxColSectionLabelHght = colSectionLayout.maxCrossAxisSpace;
145
+ this.maxColLabelLgth = this.colTermLabelLgth + (this.maxColSectionLabelHght ? this.colSectionGap + this.maxColSectionLabelHght : 0);
146
+ this.totalColWdth = cellSize * colData.colCount;
147
+ measureSvg.remove();
148
+ this.getPlotDimensions();
149
+ this.getAxisLabelPositions(rowData, colData, cellSize);
150
+ this.setColorScale(settings, data.colorScale);
151
+ this.getDotPositions(data.data, cellSize, settings);
152
+ }
153
+ getSectionLabelLayout(sections, cellSize, measureSvg, isYaxis) {
154
+ const rotateFlags = [];
155
+ const widthCache = /* @__PURE__ */ new Map();
156
+ let maxCrossAxisSpace = 0;
157
+ for (const section of sections) {
158
+ const label = section.id || "";
159
+ let labelWidth = 0;
160
+ if (label) {
161
+ if (!widthCache.has(label)) widthCache.set(label, getMaxLabelWidth(measureSvg, [label]));
162
+ labelWidth = widthCache.get(label) || 0;
163
+ }
164
+ const sectionSpan = section.terms.length * cellSize;
165
+ const rotate = isYaxis ? labelWidth <= sectionSpan : labelWidth > sectionSpan;
166
+ rotateFlags.push(rotate);
167
+ const crossAxisSpace = rotate ? isYaxis ? this.labelFontPx : labelWidth : isYaxis ? labelWidth : this.labelFontPx;
168
+ maxCrossAxisSpace = Math.max(maxCrossAxisSpace, crossAxisSpace);
169
+ }
170
+ return { rotateFlags, maxCrossAxisSpace };
171
+ }
172
+ getPlotDimensions() {
173
+ const plotDim = {
174
+ svg: {
175
+ width: this.hoziPad + this.maxRowLabelLgth + this.totalColWdth + this.hoziPad,
176
+ height: this.topPad + this.totalRowHght + this.maxColLabelLgth + this.bottomPad
177
+ },
178
+ rowLabels: {
179
+ x: this.hoziPad + this.maxRowLabelLgth,
180
+ y: this.topPad
181
+ },
182
+ colLabels: {
183
+ x: 0,
184
+ y: this.topPad + this.totalRowHght
185
+ }
186
+ };
187
+ this.viewData.plotDim = plotDim;
188
+ }
189
+ getDefaultViewData() {
190
+ return {
191
+ plotDim: {
192
+ svg: { width: 0, height: 0 },
193
+ rowLabels: { x: 0, y: 0 },
194
+ colLabels: { x: 0, y: 0 }
195
+ },
196
+ rowLabels: [],
197
+ colLabels: [],
198
+ rowSectionLabels: [],
199
+ colSectionLabels: [],
200
+ rowSectionLines: [],
201
+ colSectionLines: [],
202
+ dotPositions: [],
203
+ colorScale: {
204
+ //TODO: If the user cannot set the min and max for color values,
205
+ // revert to colorScale = scale
206
+ scale: () => "",
207
+ absMin: 0,
208
+ absMax: 0
209
+ }
210
+ };
211
+ }
212
+ getAxisLabelPositions(rowData, colData, cellSize) {
213
+ const rowSectionLineX = -(this.rowTermLabelLgth + this.sectionGap / 2);
214
+ const rowSectionLabelGap = this.sectionGap / 2;
215
+ const rowSectionRotateExtraGap = this.labelFontPx / 2 + 1;
216
+ const colTermY = this.labelFontPx;
217
+ const colTermBandDepth = colTermY + this.colTermLabelLgth;
218
+ const colSectionBandStart = colTermBandDepth + (this.maxColSectionLabelHght ? this.colSectionGap : 0);
219
+ const colSectionLineY = Math.max(0, colSectionBandStart - this.colSectionLabelLineGap);
220
+ const colSectionLineInset = Math.max(this.minColSectionLineInset, cellSize * 0.06);
221
+ this.lastY = 0;
222
+ this.lastX = this.hoziPad + this.maxRowLabelLgth;
223
+ this.viewData.rowLabels = [];
224
+ this.viewData.colLabels = [];
225
+ this.viewData.rowSectionLabels = [];
226
+ this.viewData.colSectionLabels = [];
227
+ this.viewData.rowSectionLines = [];
228
+ this.viewData.colSectionLines = [];
229
+ for (const [rowSectionIndex, section] of rowData.sections.entries()) {
230
+ const sectionStartY = this.lastY;
231
+ for (const term of section.terms) {
232
+ const row = {
233
+ x: 0,
234
+ y: this.lastY + cellSize / 2,
235
+ label: term.label || term.id
236
+ };
237
+ this.viewData.rowLabels.push(row);
238
+ this.lastY += cellSize;
239
+ }
240
+ const sectionCenterY = sectionStartY + section.terms.length * cellSize / 2;
241
+ const sectionEndY = sectionStartY + section.terms.length * cellSize;
242
+ const rotate = this.rowSectionRotateFlags[rowSectionIndex];
243
+ this.viewData.rowSectionLabels.push({
244
+ x: rowSectionLineX - rowSectionLabelGap - (rotate ? rowSectionRotateExtraGap : 0),
245
+ y: sectionCenterY,
246
+ label: section.id,
247
+ rotate
248
+ });
249
+ this.viewData.rowSectionLines.push({
250
+ x: rowSectionLineX,
251
+ y1: sectionStartY + cellSize / 2,
252
+ y2: sectionEndY - cellSize / 2
253
+ });
254
+ }
255
+ for (const [colSectionIndex, section] of colData.sections.entries()) {
256
+ const sectionStartX = this.lastX;
257
+ for (const term of section.terms) {
258
+ const col = {
259
+ x: this.lastX + cellSize / 2,
260
+ y: colTermY,
261
+ label: term.label || term.id
262
+ };
263
+ this.viewData.colLabels.push(col);
264
+ this.lastX += cellSize;
265
+ }
266
+ const sectionCenterX = sectionStartX + section.terms.length * cellSize / 2;
267
+ const rotate = this.colSectionRotateFlags[colSectionIndex];
268
+ const colSectionLabelY = colSectionLineY + this.colSectionLabelGap + (rotate ? 0 : this.labelFontPx / 2);
269
+ this.viewData.colSectionLabels.push({
270
+ x: sectionCenterX,
271
+ y: colSectionLabelY,
272
+ label: section.id,
273
+ rotate
274
+ });
275
+ this.viewData.colSectionLines.push({
276
+ y: colSectionLineY,
277
+ x1: sectionStartX + colSectionLineInset,
278
+ x2: this.lastX - colSectionLineInset
279
+ });
280
+ }
281
+ }
282
+ setColorScale(settings, colorScaleData) {
283
+ const scale = linear().domain([colorScaleData.min, colorScaleData.max]).range([settings.startColor, settings.stopColor]);
284
+ this.viewData.colorScale = {
285
+ scale,
286
+ absMin: colorScaleData.min,
287
+ absMax: colorScaleData.max
288
+ };
289
+ }
290
+ getDotPositions(data, cellSize, settings) {
291
+ const startX = this.hoziPad + this.maxRowLabelLgth;
292
+ const startY = this.topPad;
293
+ this.lastY = startY;
294
+ this.lastX = startX;
295
+ for (const [i, row] of data.entries()) {
296
+ for (const dot of row) {
297
+ const dotPos = {
298
+ x: this.lastX + cellSize / 2,
299
+ y: this.lastY + cellSize / 2,
300
+ size: dot.dotSize,
301
+ color: this.viewData.colorScale.scale(dot?.colorValue) ?? "white",
302
+ row: dot.row,
303
+ rowSection: dot.rowSection,
304
+ column: dot.column,
305
+ colSection: dot.colSection,
306
+ tipData: [
307
+ {
308
+ label: dot.rowSection,
309
+ value: dot.row
310
+ },
311
+ {
312
+ label: dot.colSection,
313
+ value: dot.column
314
+ },
315
+ {
316
+ // Show the color value
317
+ label: capitalizeFirstLetter(settings.gradientMethod),
318
+ value: roundValueAuto(dot.colorValue) ?? "N/A"
319
+ },
320
+ {
321
+ // Show the size value
322
+ label: capitalizeFirstLetter(settings.sizeMethod),
323
+ value: roundValueAuto(dot.sizeValue) ?? "N/A"
324
+ }
325
+ ]
326
+ };
327
+ this.viewData.dotPositions.push(dotPos);
328
+ this.lastX += cellSize;
329
+ }
330
+ this.lastX = startX;
331
+ this.lastY = startY + (i + 1) * cellSize;
332
+ }
333
+ }
334
+ };
335
+
336
+ // plots/aggregateMatrix/view/LegendRender.ts
337
+ var LegendRender = class {
338
+ constructor(ag) {
339
+ this.xStart = 15;
340
+ this.ag = ag;
341
+ }
342
+ render(viewData, div) {
343
+ const settings = this.ag.state.config.settings.aggregateMatrix;
344
+ const colorScaleSvg = div.append("svg").style("display", "block").attr("height", 100);
345
+ const dotScaleSvg = div.append("svg").style("display", "block").attr("height", settings.maxDotSize + 20 + 50);
346
+ this.renderColorScale(viewData.colorScale, settings, colorScaleSvg);
347
+ this.renderDotScaleRef(dotScaleSvg, settings);
348
+ }
349
+ renderColorScale(colorScale, settings, svg) {
350
+ svg.append("text").attr("x", this.xStart).attr("y", 20).style("font-weight", "bold").style("font-size", "0.8em").text(capitalizeFirstLetter(settings.gradientMethod));
351
+ new ColorScale({
352
+ holder: svg,
353
+ domain: colorScale.scale.domain(),
354
+ colors: [settings.startColor, settings.stopColor],
355
+ barheight: 20,
356
+ barwidth: 200,
357
+ position: `${this.xStart + 10}, 35`,
358
+ setColorsCallback: (val, idx) => {
359
+ const hexColor = rgb(val).formatHex();
360
+ const colorKey = idx == 0 ? "startColor" : "stopColor";
361
+ this.ag.app.dispatch({
362
+ type: "plot_edit",
363
+ id: this.ag.id,
364
+ config: {
365
+ settings: {
366
+ aggregateMatrix: {
367
+ [colorKey]: hexColor
368
+ }
369
+ }
370
+ }
371
+ });
372
+ }
373
+ });
374
+ }
375
+ renderDotScaleRef(svg, settings) {
376
+ new LegendCircleReference({
377
+ g: svg.append("g").attr("transform", `translate(${this.xStart}, 15)`),
378
+ inputMax: settings.dotInputMax,
379
+ inputMin: settings.dotInputMin,
380
+ maxRadius: settings.maxDotSize,
381
+ minRadius: settings.minDotSize,
382
+ isAscending: true,
383
+ title: capitalizeFirstLetter(settings.sizeMethod),
384
+ menu: {
385
+ minMaxLabel: "pixels",
386
+ callback: async (obj) => {
387
+ const { min, max } = obj;
388
+ const isValid = validateMinMax(settings, min, max);
389
+ if (isValid !== null) {
390
+ alert(isValid);
391
+ return;
392
+ }
393
+ this.ag.app.dispatch({
394
+ type: "plot_edit",
395
+ id: this.ag.id,
396
+ config: {
397
+ settings: {
398
+ aggregateMatrix: {
399
+ minDotSize: min,
400
+ maxDotSize: max
401
+ }
402
+ }
403
+ }
404
+ });
405
+ }
406
+ }
407
+ });
408
+ }
409
+ };
410
+
411
+ // plots/aggregateMatrix/view/AggMatrixView.ts
412
+ var AggMatrixView = class {
413
+ constructor(ag) {
414
+ this.ag = ag;
415
+ this.legendRender = new LegendRender(ag);
416
+ }
417
+ render(viewData) {
418
+ this.initDom(viewData.plotDim);
419
+ this.renderAxesLabels(
420
+ viewData.colLabels,
421
+ viewData.rowLabels,
422
+ viewData.colSectionLabels,
423
+ viewData.rowSectionLabels,
424
+ viewData.colSectionLines,
425
+ viewData.rowSectionLines
426
+ );
427
+ this.renderDots(viewData.dotPositions);
428
+ this.legendRender.render(viewData, this.dom.legendDiv);
429
+ }
430
+ initDom(plotDim) {
431
+ const mainDiv = this.ag.dom.mainDiv;
432
+ mainDiv.selectAll("*").remove();
433
+ const svg = mainDiv.append("svg").attr("width", plotDim.svg.width).attr("height", plotDim.svg.height).attr("data-testid", "sjpp-ag-matrix-svg");
434
+ const rowLabels = svg.append("g").attr("class", "sjpp-ag-matrix-row-labels").attr("transform", `translate(${plotDim.rowLabels.x}, ${plotDim.rowLabels.y}) `);
435
+ const colLabels = svg.append("g").attr("class", "sjpp-ag-matrix-col-labels").attr("transform", `translate(${plotDim.colLabels.x}, ${plotDim.colLabels.y})`);
436
+ const legendDiv = mainDiv.append("div").attr("class", "sjpp-ag-matrix-legend").attr("data-testid", "sjpp-ag-matrix-legend").style("vertical-align", "top").style("display", "inline-block").style("padding", `${this.ag.viewModel.topPad}px ${this.ag.viewModel.hoziPad}px`);
437
+ this.dom = {
438
+ svg,
439
+ rowLabels,
440
+ colLabels,
441
+ legendDiv,
442
+ tip: new Menu({ padding: "3px" })
443
+ };
444
+ }
445
+ renderAxesLabels(colLabels, rowLabels, colSectionLabels, rowSectionLabels, colSectionLines, rowSectionLines) {
446
+ const { rowLabels: rowLabelsGroup, colLabels: colLabelsGroup } = this.dom;
447
+ rowLabelsGroup.selectAll("text").data(rowLabels).enter().append("text").attr("class", "sjpp-ag-matrix-row-label").attr("text-anchor", "end").attr("dominant-baseline", "middle").attr("fill", "#3f3f46").attr("font-size", 12).attr("font-weight", 400).attr("transform", (d) => `translate(${d.x}, ${d.y})`).text((d) => d.label);
448
+ rowLabelsGroup.selectAll(".sjpp-ag-matrix-row-section-label").data(rowSectionLabels).enter().append("text").attr("class", "sjpp-ag-matrix-row-section-label").attr("text-anchor", (d) => d.rotate ? "middle" : "end").attr("dominant-baseline", "middle").attr("fill", "#111827").attr("font-size", 12).attr("letter-spacing", "0.02em").attr(
449
+ "transform",
450
+ (d) => d.rotate ? `translate(${d.x}, ${d.y}) rotate(-90)` : `translate(${d.x}, ${d.y})`
451
+ ).text((d) => d.label);
452
+ rowLabelsGroup.selectAll(".sjpp-ag-matrix-row-section-line").data(rowSectionLines).enter().append("line").attr("class", "sjpp-ag-matrix-row-section-line").attr("stroke", "#6b7280").attr("stroke-width", 1).attr("opacity", 0.9).attr("x1", (d) => d.x).attr("x2", (d) => d.x).attr("y1", (d) => d.y1).attr("y2", (d) => d.y2);
453
+ colLabelsGroup.selectAll("text").data(colLabels).enter().append("text").attr("class", "sjpp-ag-matrix-col-label").attr("text-anchor", "end").attr("dominant-baseline", "middle").attr("fill", "#3f3f46").attr("font-size", 12).attr("font-weight", 400).attr("transform", (d) => `translate(${d.x}, ${d.y}) rotate(-90)`).text((d) => d.label);
454
+ colLabelsGroup.selectAll(".sjpp-ag-matrix-col-section-label").data(colSectionLabels).enter().append("text").attr("class", "sjpp-ag-matrix-col-section-label").attr("text-anchor", (d) => d.rotate ? "end" : "middle").attr("dominant-baseline", "middle").attr("fill", "#111827").attr("font-size", 12).attr("letter-spacing", "0.02em").attr(
455
+ "transform",
456
+ (d) => d.rotate ? `translate(${d.x}, ${d.y}) rotate(-90)` : `translate(${d.x}, ${d.y})`
457
+ ).text((d) => d.label);
458
+ colLabelsGroup.selectAll(".sjpp-ag-matrix-col-section-line").data(colSectionLines).enter().append("line").attr("class", "sjpp-ag-matrix-col-section-line").attr("stroke", "#6b7280").attr("stroke-width", 1).attr("opacity", 0.9).attr("x1", (d) => d.x1).attr("x2", (d) => d.x2).attr("y1", (d) => d.y).attr("y2", (d) => d.y);
459
+ }
460
+ renderDots(dotPositions) {
461
+ for (const dot of dotPositions) {
462
+ this.dom.svg.append("circle").attr("class", "sjpp-ag-matrix-dot").attr("data-testid", `sjpp-ag-matrix-dot-${dot.row}-${dot.column}`).attr("cx", dot.x).attr("cy", dot.y).attr("r", dot.size).attr("fill", dot.color).on("mouseover", (event) => {
463
+ this.dom.tip.clear().show(event.clientX, event.clientY);
464
+ const table = table2col({ holder: this.dom.tip.d });
465
+ for (const v of dot.tipData) {
466
+ addTableRow(table, v.label, v.value);
467
+ }
468
+ }).on("mouseout", () => {
469
+ this.dom.tip.clear().hide();
470
+ }).on("click", () => {
471
+ const config = this.ag.state.config;
472
+ const colTerms = config.columns?.[dot.colSection] || [];
473
+ const colTerm = colTerms.find((term) => term.id === dot.column);
474
+ if (!colTerm) return;
475
+ if (colTerm.type !== PSEUDOBULK) return;
476
+ const tmp = structuredClone(colTerm);
477
+ const idName = `geneExpression ${dot.row} ${dot.column}`;
478
+ tmp.gene = dot.row;
479
+ tmp.category = dot.column;
480
+ tmp.id = idName;
481
+ tmp.name = idName;
482
+ this.ag.app.dispatch({
483
+ type: "plot_create",
484
+ config: {
485
+ chartType: "summary",
486
+ term: {
487
+ term: tmp,
488
+ q: { mode: "continuous" }
489
+ }
490
+ }
491
+ });
492
+ });
493
+ }
494
+ }
495
+ };
496
+ function addTableRow(table, label, value) {
497
+ const [td1, td2] = table.addRow();
498
+ td1.text(label);
499
+ td2.text(value);
500
+ }
501
+
502
+ // plots/aggregateMatrix/view/setControls.ts
503
+ async function setControls(controlsDiv, ag) {
504
+ const settings = ag.state.config.settings.aggregateMatrix;
505
+ const chartType = ag.type;
506
+ const gradientLabel = capitalizeFirstLetter(settings.gradientMethod);
507
+ const inputs = [
508
+ {
509
+ label: `${gradientLabel} start color`,
510
+ type: "color",
511
+ chartType,
512
+ settingsKey: "startColor"
513
+ },
514
+ {
515
+ label: `${gradientLabel} stop color`,
516
+ type: "color",
517
+ chartType,
518
+ settingsKey: "stopColor"
519
+ },
520
+ {
521
+ label: "Min dot size",
522
+ title: "Set the minimum dot size. Number must be between 2 and 35",
523
+ type: "number",
524
+ chartType,
525
+ settingsKey: "minDotSize",
526
+ step: 1,
527
+ max: settings.dotInputMax,
528
+ min: settings.dotInputMin,
529
+ width: 55,
530
+ debounceInterval: 300,
531
+ processInput: (val) => {
532
+ const currentSettings = ag.state.config.settings.aggregateMatrix;
533
+ const isValid = validateMinMax(currentSettings, val, currentSettings.maxDotSize);
534
+ if (isValid !== null) {
535
+ alert(isValid);
536
+ return currentSettings.minDotSize;
537
+ }
538
+ return val;
539
+ }
540
+ },
541
+ {
542
+ label: "Max dot size",
543
+ title: "Set the maximum dot size. Number must be between 2 and 35",
544
+ type: "number",
545
+ chartType,
546
+ settingsKey: "maxDotSize",
547
+ step: 1,
548
+ max: settings.dotInputMax,
549
+ min: settings.dotInputMin,
550
+ width: 55,
551
+ debounceInterval: 300,
552
+ processInput: (val) => {
553
+ const currentSettings = ag.state.config.settings.aggregateMatrix;
554
+ const isValid = validateMinMax(currentSettings, currentSettings.minDotSize, val);
555
+ if (isValid !== null) {
556
+ alert(isValid);
557
+ return currentSettings.maxDotSize;
558
+ }
559
+ return val;
560
+ }
561
+ }
562
+ ];
563
+ ag.components.controls = await controlsInit({
564
+ app: ag.app,
565
+ id: ag.id,
566
+ holder: controlsDiv,
567
+ inputs
568
+ });
569
+ ag.components.controls.on("downloadClick.aggregateMatrix", async (event) => {
570
+ const name = ag.state.config.name || "Aggregate matrix";
571
+ const svg = ag.dom.mainDiv.select("svg");
572
+ const chartImages = [{ name, svg }];
573
+ new DownloadMenu(chartImages, name).show(event.clientX, event.clientY);
574
+ });
575
+ }
576
+
577
+ // plots/aggregateMatrix/AggregateMatrix.ts
578
+ var AggregateMatrix = class _AggregateMatrix extends PlotBase {
579
+ static {
580
+ this.type = "aggregateMatrix";
581
+ }
582
+ constructor(opts, api) {
583
+ super(opts, api);
584
+ this.type = _AggregateMatrix.type;
585
+ this.components = { controls: {} };
586
+ const dom = super.getStandardDomLayout(opts.holder);
587
+ this.dom = {
588
+ holder: opts.holder,
589
+ controls: dom.controls.attr("data-testid", "sjpp-ag-matrix-controls"),
590
+ errorDiv: dom.errdiv.attr("data-testid", "sjpp-ag-matrix-error"),
591
+ loadingDiv: dom.loadingDiv.attr("data-testid", "sjpp-ag-matrix-loading"),
592
+ mainDiv: dom.charts.attr("data-testid", "sjpp-ag-matrix-main").style("padding", "10px")
593
+ };
594
+ if (opts.header) opts.header.html(`AGGREGATE MATRIX`).style("font-size", "0.9em");
595
+ }
596
+ getState(appState) {
597
+ const config = appState.plots.find((p) => p.id === this.id);
598
+ if (!config) {
599
+ throw new Error(
600
+ `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`
601
+ );
602
+ }
603
+ const parentConfig = appState.plots.find((p) => p.id === this.parentId);
604
+ const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
605
+ return {
606
+ termfilter,
607
+ config
608
+ };
609
+ }
610
+ async init() {
611
+ this.model = new AggMatrixModel(this);
612
+ this.viewModel = new AggMatrixViewModel(this);
613
+ this.view = new AggMatrixView(this);
614
+ }
615
+ async main() {
616
+ if (!this.model) throw new Error(`Model not initialized`);
617
+ if (!this.viewModel) throw new Error(`ViewModel not initialized`);
618
+ if (!this.view) throw new Error(`View not initialized`);
619
+ super.toggleLoadingDiv();
620
+ try {
621
+ const data = await this.model.getData();
622
+ if (!data || data.error) {
623
+ super.toggleLoadingDiv("none");
624
+ super.printError(data?.error || "No data returned from server");
625
+ return;
626
+ }
627
+ this.dom.controls.selectAll("*").remove();
628
+ await setControls(this.dom.controls, this);
629
+ this.viewModel.processData(data);
630
+ } catch (e) {
631
+ if (e instanceof Error) console.error(`${e.message || e} [AggregateMatrix main()]`);
632
+ else if (e.stack) console.log(e.stack);
633
+ super.toggleLoadingDiv("none");
634
+ super.printError(e.message || e);
635
+ return;
636
+ }
637
+ this.view.render(this.viewModel.viewData);
638
+ super.toggleLoadingDiv("none");
639
+ }
640
+ };
641
+ var aggMatrixInit = getCompInit(AggregateMatrix);
642
+ var componentInit = aggMatrixInit;
643
+ function getPlotConfig(opts) {
644
+ validatePlotConfig(opts);
645
+ const config = {
646
+ hidePlotFilter: true,
647
+ settings: {
648
+ aggregateMatrix: getAggregateMatrixSettings(opts?.settings?.aggregateMatrix)
649
+ }
650
+ };
651
+ return copyMerge(config, opts);
652
+ }
653
+ function validatePlotConfig(config) {
654
+ if (!config || typeof config !== "object") throw new Error(`Invalid config provided for AggregateMatrix plot`);
655
+ if (!config.rows || !Object.keys(config.rows).length) throw new Error(`No rows provided for AggregateMatrix plot`);
656
+ if (!config.columns || !Object.keys(config.columns).length) throw new Error(`No columns provided for AggregateMatrix plot`);
657
+ }
658
+ export {
659
+ AggregateMatrix,
660
+ aggMatrixInit,
661
+ componentInit,
662
+ getPlotConfig,
663
+ validatePlotConfig
664
+ };
665
+ //# sourceMappingURL=AggregateMatrix-5TBUMFE5.js.map