@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.
- package/dist/2dmaf-6CEBP4SA.js +1366 -0
- package/dist/AIProjectAdmin-2CKKFC3A.js +951 -0
- package/dist/AggregateMatrix-5TBUMFE5.js +665 -0
- package/dist/AppHeader-5YBPWF44.js +829 -0
- package/dist/BoxPlot-UOJS5SJV.js +1210 -0
- package/dist/CorrelationVolcano-KX6JPZMT.js +613 -0
- package/dist/Cuminc-TLOOLZWR.js +1208 -0
- package/dist/DE-HUQLQ2Z3.js +87 -0
- package/dist/DEinput-WWUISAF2.js +404 -0
- package/dist/DifferentialAnalysis-6DTAGCEY.js +237 -0
- package/dist/Disco-P6ZLPYLF.js +3388 -0
- package/dist/Disco.UI-WGTMAFK2.js +242 -0
- package/dist/DmrPlot-3FRU5KUK.js +636 -0
- package/dist/GB-NWOBARL3.js +1390 -0
- package/dist/GSEA-DEEUAAMI.js +850 -0
- package/dist/GeneExpInput-6QWGEAFV.js +361 -0
- package/dist/Geomap-6HT2B7RH.js +83 -0
- package/dist/HicApp-PCNOUULF.js +2244 -0
- package/dist/IDCViewer-H3QPXVM3.js +10811 -0
- package/dist/NumBinaryEditor-IU6OLMKN.js +278 -0
- package/dist/NumBinaryEditor.unit.spec-YUPUILIV.js +311 -0
- package/dist/NumContEditor-KFDA76QN.js +104 -0
- package/dist/NumContEditor.unit.spec-QBOT5QHU.js +163 -0
- package/dist/NumCustomBinEditor-EOSTEXLB.js +32 -0
- package/dist/NumCustomBinEditor.unit.spec-B46XWFYH.js +396 -0
- package/dist/NumDiscreteEditor-Y4EAADXC.js +169 -0
- package/dist/NumDiscreteEditor.unit.spec-SJGHLWSM.js +232 -0
- package/dist/NumRegularBinEditor-3BNG7DIN.js +32 -0
- package/dist/NumRegularBinEditor.unit.spec-KM45QXXG.js +277 -0
- package/dist/NumSplineEditor-K4KPDC4S.js +209 -0
- package/dist/NumSplineEditor.unit.spec-TKQP5XTS.js +223 -0
- package/dist/NumericDensity-Z6JFVN3D.js +32 -0
- package/dist/NumericDensity.unit.spec-YEYBVLEP.js +417 -0
- package/dist/NumericHandler-ITT6HMPN.js +33 -0
- package/dist/NumericHandler.unit.spec-QVONMXY4.js +213 -0
- package/dist/ProteomeInput-PRS3DEMZ.js +387 -0
- package/dist/Regression-LJJJBBT6.js +1413 -0
- package/dist/Regression-LJJJBBT6.js.map +7 -0
- package/dist/RunChart2-AMM2JFF5.js +749 -0
- package/dist/SC-F7IE66VZ.js +1106 -0
- package/dist/Violin-RJ6OJZ4F.js +1073 -0
- package/dist/Volcano-BJA5HN5Y.js +1414 -0
- package/dist/WSIViewer-RJZGRUIR.js +26194 -0
- package/dist/Wsi-DXP6KOQA.js +232 -0
- package/dist/WsiSamplesPlot-2IAWV2B6.js +159 -0
- package/dist/adSandbox-RGWOIV3W.js +32 -0
- package/dist/animatedBubbleChart-J4Q2NAEW.js +546 -0
- package/dist/app-3QXNR4VG.js +31 -0
- package/dist/app-B4B7YNP3.js +41 -0
- package/dist/app.js +12 -12
- package/dist/bam-LRUMN45P.js +875 -0
- package/dist/barchart-L2G6GEHK.js +41 -0
- package/dist/barchart2-DWNVAZAJ.js +308 -0
- package/dist/block-TVEVAXNP.js +6248 -0
- package/dist/block.init-YOHAKPRI.js +32 -0
- package/dist/block.mds.expressionrank-PU6JH4W5.js +353 -0
- package/dist/block.mds.geneboxplot-WYYFDNE3.js +822 -0
- package/dist/block.mds.junction-4WCTL7Y4.js +1538 -0
- package/dist/block.mds.svcnv-MR3VCYUW.js +6795 -0
- package/dist/block.svg-LR3Y4ZO7.js +158 -0
- package/dist/block.tk.aicheck-A5AWKJZI.js +277 -0
- package/dist/block.tk.ase-AQBBAQEH.js +359 -0
- package/dist/block.tk.bam-QBTA2O3V.js +1900 -0
- package/dist/block.tk.bedgraphdot-4ALZG2MY.js +378 -0
- package/dist/block.tk.bigwig.ui-32W6XW37.js +205 -0
- package/dist/block.tk.hicstraw-PKBHBAG2.js +817 -0
- package/dist/block.tk.junction-AO5CXUCU.js +2357 -0
- package/dist/block.tk.junction.textmatrixui-RORVUIPI.js +193 -0
- package/dist/block.tk.ld-TNBSR4FT.js +93 -0
- package/dist/block.tk.menu-QDJO54J5.js +1023 -0
- package/dist/block.tk.pgv-6222WWYR.js +937 -0
- package/dist/brainImaging-2TPE7MXB.js +426 -0
- package/dist/brainImaging-2TPE7MXB.js.map +7 -0
- package/dist/brainRegions-KTFH6DE2.js +215 -0
- package/dist/bubbleHeatmap-LNXZLFY6.js +377 -0
- package/dist/cellTypeBubbleHeatmap-SRHUNX3S.js +277 -0
- package/dist/chunk-3TXVDBGN.js +626 -0
- package/dist/chunk-4HLHKBHP.js +274 -0
- package/dist/chunk-5GG7Q2ZG.js +397 -0
- package/dist/chunk-5HVAVJKW.js +518 -0
- package/dist/chunk-5HVAVJKW.js.map +7 -0
- package/dist/chunk-5PMFCQKC.js +98 -0
- package/dist/chunk-67URJYN7.js +84 -0
- package/dist/chunk-67URJYN7.js.map +7 -0
- package/dist/chunk-6AKSOLBX.js +5071 -0
- package/dist/chunk-6AKSOLBX.js.map +7 -0
- package/dist/chunk-6X7PP7A4.js +2126 -0
- package/dist/chunk-A3EDLRUN.js +54 -0
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- package/dist/chunk-EO6M3LY3.js +339 -0
- package/dist/chunk-EO6M3LY3.js.map +7 -0
- package/dist/chunk-F4PMOAQK.js +494 -0
- package/dist/chunk-FISQTHD4.js +2327 -0
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- package/dist/chunk-FXT2XM4E.js.map +7 -0
- package/dist/chunk-HIWTGMTE.js +1721 -0
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- package/dist/chunk-KLWSW6CC.js +203 -0
- package/dist/chunk-KNNSOOTG.js +194 -0
- package/dist/chunk-KTPXQH2N.js +170 -0
- package/dist/chunk-LGKXSWY4.js +276 -0
- package/dist/chunk-LP2GIXVK.js +4274 -0
- package/dist/chunk-M2ZZL5EV.js +2669 -0
- package/dist/chunk-M2ZZL5EV.js.map +7 -0
- package/dist/chunk-MBHERRJR.js +302 -0
- package/dist/chunk-MLYQDJUQ.js +480 -0
- package/dist/chunk-NBGDLLMX.js +446 -0
- package/dist/chunk-OPMMU6DQ.js +183 -0
- package/dist/chunk-OPMMU6DQ.js.map +7 -0
- package/dist/chunk-P3JEXVBT.js +50 -0
- package/dist/chunk-PZPPJY4K.js +34 -0
- package/dist/chunk-Q6JF4ZLT.js +141 -0
- package/dist/chunk-QF5IH7PC.js +263 -0
- package/dist/chunk-QJ6SO7CF.js +465 -0
- package/dist/chunk-QQUOVIOM.js +2899 -0
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- package/dist/chunk-SNCZRDS5.js +557 -0
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- package/dist/chunk-SPDNUC76.js +70 -0
- package/dist/chunk-T3663ZQL.js +37 -0
- package/dist/chunk-TSK4ZTFK.js +340 -0
- package/dist/chunk-USW6WRDZ.js +217 -0
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- package/dist/chunk-XE6E526E.js +129 -0
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- package/dist/chunk-YCECQV3T.js +160 -0
- package/dist/chunk-YROOKO3Q.js +1954 -0
- package/dist/chunk-YROOKO3Q.js.map +7 -0
- package/dist/chunk-Z4NADGZX.js +243 -0
- package/dist/chunk-Z53KOPRJ.js +102 -0
- package/dist/cohort-U7M6Q2UX.js +69 -0
- package/dist/condition-EGAV2PMJ.js +326 -0
- package/dist/controls-PTMYWUZV.js +33 -0
- package/dist/controls.config-DOA6PTP2.js +33 -0
- package/dist/correlation-Y3EL6GB7.js +94 -0
- package/dist/customdata.inputui-4NDDG6FL.js +283 -0
- package/dist/dataDownload-EQGUAOK2.js +328 -0
- package/dist/databrowser.ui-ABGOJUWQ.js +424 -0
- package/dist/dictionary-YOLLEDE5.js +112 -0
- package/dist/dnaMethylation-JZT63UHO.js +32 -0
- package/dist/dnaMethylation.integration.spec-EATCABJW.js +197 -0
- package/dist/dofetch-YNBIUFV5.js +48 -0
- package/dist/e2pca-RD6COCRL.js +343 -0
- package/dist/ep-BAI7WUET.js +1248 -0
- package/dist/expclust.gdc.spec-LKV2CQA5.js +301 -0
- package/dist/facet-X3SXQIAC.js +518 -0
- package/dist/gb-K324K7XB.js +80 -0
- package/dist/geneExpClustering-BJD5U3KG.js +243 -0
- package/dist/geneExpression-2TK3XLZ5.js +310 -0
- package/dist/geneExpression-F6NRTHZ4.js +32 -0
- package/dist/geneExpression.unit.spec-IFZN3J6A.js +96 -0
- package/dist/geneORA-DUEP735U.js +272 -0
- package/dist/geneRanking-LURDNT7L.js +547 -0
- package/dist/geneVariant-EAVCWQAZ.js +35 -0
- package/dist/geneVariant-IZTFYAG6.js +284 -0
- package/dist/geneVariant-IZTFYAG6.js.map +7 -0
- package/dist/geneVariant.integration.spec-LHL4ERFO.js +192 -0
- package/dist/genefusion.ui-4T5R7DT7.js +302 -0
- package/dist/geneset-3PWXPBG2.js +202 -0
- package/dist/genomeBrowser.spec-5SEN7R2P.js +275 -0
- package/dist/grin2-EXBG7TMS.js +1136 -0
- package/dist/grin2-XIXVFVWO.js +69 -0
- package/dist/hierCluster-5XQIWXAY.js +57 -0
- package/dist/hierCluster-I4TAQWPF.js +53 -0
- package/dist/hierCluster.config-T7HVAWES.js +34 -0
- package/dist/hierCluster.integration.spec-XWX43K4D.js +482 -0
- package/dist/hierCluster.interactivity-MYIDHFSL.js +48 -0
- package/dist/hierCluster.renderers-YRXA5ZUK.js +19 -0
- package/dist/imagePlot-4JQB6JUG.js +155 -0
- package/dist/importPlot-D3MXCCLN.js +8 -0
- package/dist/isoformExpression-WNGGUVIZ.js +34 -0
- package/dist/isoformExpression.unit.spec-NVJ5TIKM.js +236 -0
- package/dist/junction-O7N57JE3.js +35 -0
- package/dist/junction.unit.spec-Z63DRTRR.js +181 -0
- package/dist/launch.adhoc-MBDRXD3B.js +36 -0
- package/dist/leftlabel.sample-IG6FOQ26.js +257 -0
- package/dist/lollipop-ZUYBLPGN.js +165 -0
- package/dist/maf-QOS5LURG.js +454 -0
- package/dist/maftimeline-FEHP2J55.js +586 -0
- package/dist/matrix-BG4J4RXA.js +57 -0
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- package/dist/matrix.cells-PTIDQVCI.js +26 -0
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- package/dist/matrix.data-FMIQRXOA.js +23 -0
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- package/dist/multivalue-OZALSBFW.js +82 -0
- package/dist/numericDictTermCluster-7PGJ7KV4.js +63 -0
- package/dist/oncomatrix-Q2EQZPLS.js +289 -0
- package/dist/oncomatrix.spec-YEQOQRPW.js +442 -0
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- package/dist/plot.app-AEUR6XGI.js +35 -0
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- package/dist/plot.disco-LUFC5GGC.js +99 -0
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- package/dist/polar2-AB6SVYRS.js +231 -0
- package/dist/profileForms-AIEHZ4GC.js +933 -0
- package/dist/profilePlot-PZDFGXKZ.js +48 -0
- package/dist/proteinView-7GWHQYXC.js +1561 -0
- package/dist/proteomeCohortCompare-BTN4HHFL.js +779 -0
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- package/dist/singleCellCellType-EZYESBVZ.js +32 -0
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- /package/dist/{summary.integration.spec-52WP6SNY.js.map → summary.integration.spec-JJDE6SRV.js.map} +0 -0
- /package/dist/{summaryInput-WUJNHCGH.js.map → summaryInput-JG4AW6FW.js.map} +0 -0
- /package/dist/{sunburst-IJ3ZG2BC.js.map → sunburst-YKB42RZX.js.map} +0 -0
- /package/dist/{survival-SQRYWGWZ.js.map → survival-3IFFTDQA.js.map} +0 -0
- /package/dist/{survival-F2B5JKOO.js.map → survival-HOFNJENX.js.map} +0 -0
- /package/dist/{svgraph-HVCMF6KI.js.map → svgraph-WFEY4ZIZ.js.map} +0 -0
- /package/dist/{svmr-PROHTMTP.js.map → svmr-44EIX7YD.js.map} +0 -0
- /package/dist/{table-3E64OJNV.js.map → table-6MKVJUNC.js.map} +0 -0
- /package/dist/{termCollection-WKT6ESMI.js.map → termCollection-6JBVQL6Y.js.map} +0 -0
- /package/dist/{summary-U3YKEMZC.js.map → termCollection-TTELZVC5.js.map} +0 -0
- /package/dist/{termCollection.unit.spec-XMOCMVER.js.map → termCollection.unit.spec-6Z7X646L.js.map} +0 -0
- /package/dist/{termCollection-MUH7P6B5.js.map → termCollectionFractionSelection-5DVIJBM5.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection.unit.spec-MG7E3EIZ.js.map → termCollectionFractionSelection.unit.spec-3HIM5BIF.js.map} +0 -0
- /package/dist/{termCollectionFractionSelection-P5G6WIJJ.js.map → tk-HSYWJCGQ.js.map} +0 -0
- /package/dist/{tk-HWUPUGOS.js.map → tk-PNOVG2XS.js.map} +0 -0
- /package/dist/{tp.ui-RRB5MJRD.js.map → tp.ui-COBBSUPB.js.map} +0 -0
- /package/dist/{tk-SBM2GN3S.js.map → tvs.dt-35AKURFI.js.map} +0 -0
- /package/dist/{tvs.dtcnv.categorical-7RJPQKMX.js.map → tvs.dtcnv.categorical-3EHXYROL.js.map} +0 -0
- /package/dist/{tvs.dtcnv.continuous-FW4ZXIYY.js.map → tvs.dtcnv.continuous-AXQ2GU6S.js.map} +0 -0
- /package/dist/{tvs.dtfusion-3GDWW3ML.js.map → tvs.dtfusion-PLJIMPNX.js.map} +0 -0
- /package/dist/{tvs.dtitd-FER4H4UO.js.map → tvs.dtitd-JS6RFBV5.js.map} +0 -0
- /package/dist/{tvs.dtsnvindel-ISEOJ5UA.js.map → tvs.dtsnvindel-MDEM5MPT.js.map} +0 -0
- /package/dist/{tvs.dtsv-JDML7EWE.js.map → tvs.dtsv-OU756YLO.js.map} +0 -0
- /package/dist/{tvs.samplelst-MJTM6GSV.js.map → tvs.samplelst-5NDICES4.js.map} +0 -0
- /package/dist/{tvs.termCollection-GMOXBJWF.js.map → tvs.termCollection-5URPDPH6.js.map} +0 -0
- /package/dist/{tvs.dt-I2ECKHQ2.js.map → vocabulary-CHCVMPK5.js.map} +0 -0
- /package/dist/{wsi.direct-IVPACPNT.js.map → wsi.direct-JSKV4H4X.js.map} +0 -0
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import {
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ColorScale,
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getCombinedTermFilter,
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getMaxLabelWidth,
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table2col
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} from "./chunk-D5PX2UDG.js";
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// plots/aggregateMatrix/model/AggMatrixModel.ts
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var AggMatrixModel = class {
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constructor(ag) {
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function getAggregateMatrixSettings(overrides = {}) {
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const mergedSettings = Object.assign({}, defaults, overrides);
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throw new Error(`Invalid min/max dot size settings: ${isValidMinMax}`);
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// plots/aggregateMatrix/viewModel/AggMatrixViewModel.ts
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var AggMatrixViewModel = class {
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constructor(ag) {
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const dotPadding = settings.maxDotSize * 1.5;
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this.rowTermLabelLgth = getMaxLabelWidth(measureSvg, [rowData.longestLabel]);
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const rowSectionLayout = this.getSectionLabelLayout(rowData.sections, cellSize, measureSvg, true);
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this.maxRowSectionLabelWdth = rowSectionLayout.maxCrossAxisSpace;
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this.maxRowLabelLgth = this.rowTermLabelLgth + (this.maxRowSectionLabelWdth ? this.sectionGap + this.maxRowSectionLabelWdth : 0);
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this.totalRowHght = cellSize * rowData.rowCount;
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const colData = data.axesLayout.columns;
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this.colTermLabelLgth = getMaxLabelWidth(measureSvg, [colData.longestLabel]);
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const colSectionLayout = this.getSectionLabelLayout(colData.sections, cellSize, measureSvg, false);
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this.colSectionRotateFlags = colSectionLayout.rotateFlags;
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this.maxColSectionLabelHght = colSectionLayout.maxCrossAxisSpace;
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this.maxColLabelLgth = this.colTermLabelLgth + (this.maxColSectionLabelHght ? this.colSectionGap + this.maxColSectionLabelHght : 0);
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this.totalColWdth = cellSize * colData.colCount;
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measureSvg.remove();
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this.getPlotDimensions();
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this.getAxisLabelPositions(rowData, colData, cellSize);
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this.setColorScale(settings, data.colorScale);
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this.getDotPositions(data.data, cellSize, settings);
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}
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getSectionLabelLayout(sections, cellSize, measureSvg, isYaxis) {
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const rotateFlags = [];
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const widthCache = /* @__PURE__ */ new Map();
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let maxCrossAxisSpace = 0;
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for (const section of sections) {
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const label = section.id || "";
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let labelWidth = 0;
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if (label) {
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if (!widthCache.has(label)) widthCache.set(label, getMaxLabelWidth(measureSvg, [label]));
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labelWidth = widthCache.get(label) || 0;
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}
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const sectionSpan = section.terms.length * cellSize;
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const rotate = isYaxis ? labelWidth <= sectionSpan : labelWidth > sectionSpan;
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rotateFlags.push(rotate);
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const crossAxisSpace = rotate ? isYaxis ? this.labelFontPx : labelWidth : isYaxis ? labelWidth : this.labelFontPx;
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maxCrossAxisSpace = Math.max(maxCrossAxisSpace, crossAxisSpace);
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}
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return { rotateFlags, maxCrossAxisSpace };
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}
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getPlotDimensions() {
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const plotDim = {
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svg: {
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width: this.hoziPad + this.maxRowLabelLgth + this.totalColWdth + this.hoziPad,
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height: this.topPad + this.totalRowHght + this.maxColLabelLgth + this.bottomPad
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},
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rowLabels: {
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x: this.hoziPad + this.maxRowLabelLgth,
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y: this.topPad
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},
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colLabels: {
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x: 0,
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y: this.topPad + this.totalRowHght
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}
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};
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this.viewData.plotDim = plotDim;
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}
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getDefaultViewData() {
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return {
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plotDim: {
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svg: { width: 0, height: 0 },
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rowLabels: { x: 0, y: 0 },
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colLabels: { x: 0, y: 0 }
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},
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rowLabels: [],
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colLabels: [],
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rowSectionLabels: [],
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colSectionLabels: [],
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rowSectionLines: [],
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colSectionLines: [],
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dotPositions: [],
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colorScale: {
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//TODO: If the user cannot set the min and max for color values,
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// revert to colorScale = scale
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scale: () => "",
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absMin: 0,
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absMax: 0
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}
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};
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}
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getAxisLabelPositions(rowData, colData, cellSize) {
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const rowSectionLineX = -(this.rowTermLabelLgth + this.sectionGap / 2);
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const rowSectionLabelGap = this.sectionGap / 2;
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const rowSectionRotateExtraGap = this.labelFontPx / 2 + 1;
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const colTermY = this.labelFontPx;
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const colTermBandDepth = colTermY + this.colTermLabelLgth;
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const colSectionBandStart = colTermBandDepth + (this.maxColSectionLabelHght ? this.colSectionGap : 0);
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const colSectionLineY = Math.max(0, colSectionBandStart - this.colSectionLabelLineGap);
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const colSectionLineInset = Math.max(this.minColSectionLineInset, cellSize * 0.06);
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this.lastY = 0;
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this.lastX = this.hoziPad + this.maxRowLabelLgth;
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this.viewData.rowLabels = [];
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this.viewData.colLabels = [];
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this.viewData.rowSectionLabels = [];
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this.viewData.colSectionLabels = [];
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this.viewData.rowSectionLines = [];
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this.viewData.colSectionLines = [];
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for (const [rowSectionIndex, section] of rowData.sections.entries()) {
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const sectionStartY = this.lastY;
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for (const term of section.terms) {
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const row = {
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x: 0,
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y: this.lastY + cellSize / 2,
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label: term.label || term.id
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};
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this.viewData.rowLabels.push(row);
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this.lastY += cellSize;
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}
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const sectionCenterY = sectionStartY + section.terms.length * cellSize / 2;
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const sectionEndY = sectionStartY + section.terms.length * cellSize;
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const rotate = this.rowSectionRotateFlags[rowSectionIndex];
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this.viewData.rowSectionLabels.push({
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x: rowSectionLineX - rowSectionLabelGap - (rotate ? rowSectionRotateExtraGap : 0),
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y: sectionCenterY,
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label: section.id,
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rotate
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});
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this.viewData.rowSectionLines.push({
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x: rowSectionLineX,
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y1: sectionStartY + cellSize / 2,
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y2: sectionEndY - cellSize / 2
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});
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}
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for (const [colSectionIndex, section] of colData.sections.entries()) {
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const sectionStartX = this.lastX;
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for (const term of section.terms) {
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const col = {
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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
|